Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.     

Persistence of high diversity in non-equilibrium ecological communities: implications for modern and fossil ecosystems

Explaining the origin and maintenance of biodiversity is critical for understanding the potential consequences of present-day environmental change on ecological communities, as well as the evolutionary history of ecosystems in the Earth's past. Much effort in theoretical ecology has focused on identifying mechanisms that promote stable coexistence of species at equilibrium. However, in a consumer-resource model of competition along an environmental gradient, high-diversity assemblages have the potential to persist in non-equilibrium states for millions of generations with very little species loss. Species' populations in such competitively accommodated communities show slow drift; if disrupted, they rapidly reorganize into alternative persistent states. Fossil examples of prolonged ecological stability lasting 1-5 Myr punctuated by rapid reorganization (e.g. brachiopods from the Permian Reef of west Texas) suggest that some palaeocommunities represent a record of periodically disrupted transient states rather than stable equilibria. The similarity between the theoretical results reported here and palaeontological data suggests that the maintenance of high-diversity communities, both in the past and present, may reflect long-duration, non-equilibrium transient dynamics. If so, this has implications for the response of such communities to present-day environmental change, as well as for the evolution of lineages in such systems.     

Transitional states in marine fisheries: adapting to predicted global change

Global climate change has the potential to substantially alter the production and community structure of marine fisheries and modify the ongoing impacts of fishing. Fish community composition is already changing in some tropical, temperate and polar ecosystems, where local combinations of warming trends and higher environmental variation anticipate the changes likely to occur more widely over coming decades. Using case studies from the Western Indian Ocean, the North Sea and the Bering Sea, we contextualize the direct and indirect effects of climate change on production and biodiversity and, in turn, on the social and economic aspects of marine fisheries. Climate warming is expected to lead to (i) yield and species losses in tropical reef fisheries, driven primarily by habitat loss; (ii) community turnover in temperate fisheries, owing to the arrival and increasing dominance of warm-water species as well as the reduced dominance and departure of cold-water species; and (iii) increased diversity and yield in Arctic fisheries, arising from invasions of southern species and increased primary production resulting from ice-free summer conditions. How societies deal with such changes will depend largely on their capacity to adapt--to plan and implement effective responses to change--a process heavily influenced by social, economic, political and cultural conditions.     

基于国家生态足迹账户的海陆养殖产品研究

海陆养殖产品是人类蛋白质营养摄取的重要来源, 而生态足迹是评价评估人类在获取蛋白质对地球生态系统和环境的影响的重要方法。本文运用国家生态足迹账户分析法核算了我国海水养殖产品和畜牧业产品2009—2014年的生态足迹及2014年的单位蛋白质生态系数。结果表明: 2009—2014年我国海水养殖产品中扇贝的人均生态足迹最高, 从0.0005 hm2增长到0.0007 hm2; 2009—2014年畜牧产品中猪肉的人均生态足迹最高, 从1.2 hm2增长到1.4 hm2; 畜牧产品的人均生态足迹普遍高于海水养殖产品, 畜牧产品人均所需的生物生产性面积是海水养殖产品的2000倍; 由2014年的单位蛋白质生态系数核算得知, 畜牧产品的平均单位蛋白质生态系数为0.1381 hm2•kg–1, 其中羊肉的蛋白质生态系数最高, 达到0.1595 hm2•kg–1, 海水养殖产品的平均单位蛋白质生态系数为0.0020 hm2•kg–1, 其中海水鱼的单位蛋白质系数仅为0.0004 hm2•kg–1。因而在获取同等条件的蛋白质营养供给时, 我们可以优先考虑海水养殖产品, 这样既能改善国民蛋白质营养供给结构, 又能降低生态环境的生态负荷, 同时也是我们发展海洋经济、经略海洋的节点。     

Robustness of norm-driven cooperation in the commons

Sustainable use of common-pool resources such as fish, water or forests depends on the cooperation of resource users that restrain their individual extraction to socially optimal levels. Empirical evidence has shown that under certain social and biophysical conditions, self-organized cooperation in the commons can evolve. Global change, however, may drastically alter these conditions. We assess the robustness of cooperation to environmental variability in a stylized model of a community that harvests a shared resource. Community members follow a norm of socially optimal resource extraction, which is enforced through social sanctioning. Our results indicate that both resource abundance and a small increase in resource variability can lead to collapse of cooperation observed in the no-variability case, while either scarcity or large variability have the potential to stabilize it. The combined effects of changes in amount and variability can reinforce or counteract each other depending on their size and the initial level of cooperation in the community. If two socially separate groups are ecologically connected through resource leakage, cooperation in one can destabilize the other. These findings provide insights into possible effects of global change and spatial connectivity, indicating that there is no simple answer as to their effects on cooperation and sustainable resource use.     

基于MaxEnt模型的大豆蚜全球潜在地理分布分析

【目的】为预测和分析大豆蚜Aphis glycines的全球潜在地理分布,研究大豆蚜分布与环境变量之间的联系。【方法】利用最大熵法生态位模型(maximum entropy niche-based modeling, MaxEnt)和地理信息系统软件ArcGIS,根据收集的大豆蚜已知分布点和环境变量,预测大豆蚜的全球潜在地理分布区,推测环境变量对大豆蚜分布的影响。【结果】结果表明,大豆蚜适生区主要分布在低海拔地区,高 度适生区集中在25°~50°N的中国、日本、韩国、朝鲜、加拿大、美国、意大利和格鲁吉亚。决定大豆蚜分布地点的关键环境变量为最暖季度降水量、最暖季度平均温度、最湿季度平均温度、最干月降水量、月平均昼夜温差和温度季节性变化标准差。【结论】大豆蚜潜在地理分布区域广泛,应在各国大豆农产品贸易时做好检验检疫工作,以防止大豆蚜的扩散。     

UV-B辐射增强对土生对齿藓(Didymodon vinealis)结皮生理代谢及光系统相关蛋白表达的影响

以中国科学院沙坡头沙漠试验研究站人工固沙植被区的土生对齿藓(Didymodon vinealis(Brid.) Zand.)结皮为试验材料,通过室内模拟UV-B 4个辐射强度[2.75(对照)、3.08、3.25和3.41 W·m-2]的处理,研究了UV-B辐射增强对土生对齿藓结皮生理代谢及光系统相关蛋白表达的影响.结果表明:随着UV-B辐射强度增加,丙二醛(MDA)含量呈增加趋势;叶绿素a荧光诱导动力学参数、可溶性蛋白质及类囊体膜蛋白表达量随着辐射强度的增加而降低,且与辐射强度呈反比.模拟UV-B辐射增强促进了土生对齿藓结皮活性氧的代谢速率,导致了膜脂过氧化,可溶性蛋白质含量减少,进而降低PSII反应中心活性,最终导致光合作用能力下降,这一结果对于进一步理解生物土壤结皮对UV-B辐射的响应机制,探索应用生物土壤结皮进行荒漠化治理具有重要的理论与实践意义.     

The effect of dilution on eco‐evolutionary dynamics of experimental microbial communities

Changing environmental conditions can infer structural modifications of predator‐prey communities. New conditions often increase mortality which reduces population sizes. Following this, predation pressure may decrease until populations are dense again. Dilution may thus have substantial impact not only on ecological but also on evolutionary dynamics because it amends population densities. Experimental studies, in which microbial populations are maintained by a repeated dilution into fresh conditions after a certain period, are extensively used approaches allowing us to obtain mechanistic insights into fundamental processes. By design, dilution, which depends on transfer volume (modifying mortality) and transfer interval (determining the time of interaction), is an inherent feature of these experiments, but often receives little attention. We further explore previously published data from a live predator‐prey (bacteria and ciliates) system which investigated eco‐evolutionary principles and apply a mathematical model to predict how various transfer volumes and transfer intervals would affect such an experiment. We find not only the ecological dynamics to be modified by both factors but also the evolutionary rates to be affected. Our work predicts that the evolution of the anti‐predator defense in the bacteria, and the evolution of the predation efficiency in the ciliates, both slow down with lower transfer volume, but speed up with longer transfer intervals. Our results provide testable hypotheses for future studies of predator‐prey systems, and we hope this work will help improve our understanding of how ecological and evolutionary processes together shape composition of microbial communities.     

Exploring the nature of ecological specialization in a coral reef fish community: morphology,diet and foraging microhabitat use

Patterns of ecological specialization offer invaluable information about ecosystems. Yet, specialization is rarely quantified across several ecological niche axes and variables beyond the link between morphological and dietary specialization have received little attention. Here, we provide a quantitative evaluation of ecological specialization in a coral reef fish assemblage (f. Acanthuridae) along one fundamental and two realized niche axes. Specifically, we examined ecological specialization in 10 surgeonfish species with regards to morphology and two realized niche axes associated with diet and foraging microhabitat utilization using a recently developed multidimensional framework. We then investigated the potential relationships between morphological and behavioural specialization. These relationships differed markedly from the traditional ecomorphological paradigm. While morphological specialization showed no relationship with dietary specialization, it exhibited a strong relationship with foraging microhabitat specialization. However, this relationship was inverted: species with specialized morphologies were microhabitat generalists, whereas generalized morphotypes were microhabitat specialists. Interestingly, this mirrors relationships found in plant–pollinator communities and may also be applicable to other ecosystems, highlighting the potential importance of including niche axes beyond dietary specialization into ecomorphological frameworks. On coral reefs, it appears that morphotypes commonly perceived as most generalized may, in fact, be specialized in exploiting flat and easily accessible microhabitats.     

Climate change and freshwater ecosystems: impacts across multiple levels of organization

Fresh waters are particularly vulnerable to climate change because (i) many species within these fragmented habitats have limited abilities to disperse as the environment changes; (ii) water temperature and availability are climate-dependent; and (iii) many systems are already exposed to numerous anthropogenic stressors. Most climate change studies to date have focused on individuals or species populations, rather than the higher levels of organization (i.e. communities, food webs, ecosystems). We propose that an understanding of the connections between these different levels, which are all ultimately based on individuals, can help to develop a more coherent theoretical framework based on metabolic scaling, foraging theory and ecological stoichiometry, to predict the ecological consequences of climate change. For instance, individual basal metabolic rate scales with body size (which also constrains food web structure and dynamics) and temperature (which determines many ecosystem processes and key aspects of foraging behaviour). In addition, increasing atmospheric CO₂ is predicted to alter molar CNP ratios of detrital inputs, which could lead to profound shifts in the stoichiometry of elemental fluxes between consumers and resources at the base of the food web. The different components of climate change (e.g. temperature, hydrology and atmospheric composition) not only affect multiple levels of biological organization, but they may also interact with the many other stressors to which fresh waters are exposed, and future research needs to address these potentially important synergies.     

Ecological effects of pharmaceuticals in aquatic systems—impacts through behavioural alterations

The study of animal behaviour is important for both ecology and ecotoxicology, yet research in these two fields is currently developing independently. Here, we synthesize the available knowledge on drug-induced behavioural alterations in fish, discuss potential ecological consequences and report results from an experiment in which we quantify both uptake and behavioural impact of a psychiatric drug on a predatory fish (Perca fluviatilis) and its invertebrate prey (Coenagrion hastulatum). We show that perch became more active while damselfly behaviour was unaffected, illustrating that behavioural effects of pharmaceuticals can differ between species. Furthermore, we demonstrate that prey consumption can be an important exposure route as on average 46% of the pharmaceutical in ingested prey accumulated in the predator. This suggests that investigations of exposure through bioconcentration, where trophic interactions and subsequent bioaccumulation of exposed individuals are ignored, underestimate exposure. Wildlife may therefore be exposed to higher levels of behaviourally altering pharmaceuticals than predictions based on commonly used exposure assays and pharmaceutical concentrations found in environmental monitoring programmes.     

A social and ecological assessment of tropical land uses at multiple scales: the Sustainable Amazon Network

Science has a critical role to play in guiding more sustainable development trajectories. Here, we present the Sustainable Amazon Network (Rede Amazônia Sustentável, RAS): a multidisciplinary research initiative involving more than 30 partner organizations working to assess both social and ecological dimensions of land-use sustainability in eastern Brazilian Amazonia. The research approach adopted by RAS offers three advantages for addressing land-use sustainability problems: (i) the collection of synchronized and co-located ecological and socioeconomic data across broad gradients of past and present human use; (ii) a nested sampling design to aid comparison of ecological and socioeconomic conditions associated with different land uses across local, landscape and regional scales; and (iii) a strong engagement with a wide variety of actors and non-research institutions. Here, we elaborate on these key features, and identify the ways in which RAS can help in highlighting those problems in most urgent need of attention, and in guiding improvements in land-use sustainability in Amazonia and elsewhere in the tropics. We also discuss some of the practical lessons, limitations and realities faced during the development of the RAS initiative so far.     

不同生境下濒危植物膝柄木幼树的生态适应性

膝柄木是我国极度濒危植物,也是广西滨海过渡带天然植被的重要组成树种.为了解光因子对膝柄木天然更新的限制影响,该文对林缘、林窗、林下三种不同光照生境下膝柄木幼树的生理和生长指标的年际变化特征进行了研究.结果表明:(1)光合有效辐射不足影响了膝柄木幼树的生长.林下幼树的地径、株高和叶面积增长量显著降低,而生长于光照充足林缘...     

Species boundaries, specialization, and the radiation of sponge-dwelling alpheid shrimp

Microevolutionary studies and natural history suggest that host-specialization has promoted the high diversity of tropical sponge-dwelling snapping shrimps (Decapoda, Alpheidae, Synalpheus ). Yet the taxonomic difficulty of this genus has precluded rigorous tests of this hypothesis. S. rathbunae Coutiére is among the most abundant invertebrates inhabiting the framework of sponges and dead coral that forms the floor of Caribbean coral reefs. Even within a small area S. rathbunae exhibits the apparently wide variation in size, color, and morphology that has long frustrated efforts to identify and define species boundaries within this large (> 100 described species) genus. Here I show that sympatric populations of this nominal species occupying different sponge hosts display clear, concordant differences in allozyme genotypes and in multivariate morphometries, confirming that the populations represent three distinct biological species. Moreover, careful field sampling revealed that the three S. rathbunce taxa and the closely related S. filidigitus Armstrong showed almost no overlap in the species of hosts occupied. Interestingly, while there was significant differentiation between Belizean and Panamanian populations of the one taxon that occurred at both sites (∼1500 km apart), these populations were recognizable as conspecific using both genetic and morphological characters. These results show that (1) diversity of Synalpheus , which is already among the most species-rich crustacean genera, is probably several times higher than currendy recognized, and (2) species of sponge-dwelling Synalpheus are highly host-specific, with related species distinctly segregated among hosts. Together with previous evidence of host race differentiation within shrimp species, these results suggest a primary role for resource specialization in the origin and/or maintenance of this group's characteristically high diversity.     

Fishing,fast growth and climate variability increase the risk of collapse

Species around the world have suffered collapses, and a key question is why some populations are more vulnerable than others. Traditional conservation biology and evidence from terrestrial species suggest that slow-growing populations are most at risk, but interactions between climate variability and harvest dynamics may alter or even reverse this pattern. Here, we test this hypothesis globally. We use boosted regression trees to analyse the influences of harvesting, species traits and climate variability on the risk of collapse (decline below a fixed threshold) across 154 marine fish populations around the world. The most important factor explaining collapses was the magnitude of overfishing, while the duration of overfishing best explained long-term depletion. However, fast growth was the next most important risk factor. Fast-growing populations and those in variable environments were especially sensitive to overfishing, and the risk of collapse was more than tripled for fast-growing when compared with slow-growing species that experienced overfishing. We found little evidence that, in the absence of overfishing, climate variability or fast growth rates alone drove population collapse over the last six decades. Expanding efforts to rapidly adjust harvest pressure to account for climate-driven lows in productivity could help to avoid future collapses, particularly among fast-growing species.     

How habitat-modifying organisms structure the food web of two coastal ecosystems

The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and West African tropical seagrass meadows. Results reveal that habitat-modifying species, through non-trophic facilitation rather than their trophic role, enhance species richness across multiple trophic levels, increase the number of interactions per species (link density), but decrease the realized fraction of all possible links within the food web (connectance). Compared to the trophic role of the most highly connected species, we found this non-trophic effects to be more important for species richness and of more or similar importance for link density and connectance. Our findings demonstrate that food webs can be fundamentally shaped by interactions outside the trophic network, yet intrinsic to the species participating in it. Better integration of non-trophic interactions in food web analyses may therefore strongly contribute to their explanatory and predictive capacity.     

模拟酸雨对福州沿江稻田水稻叶片碳氮磷含量及其生态化学计量学特征的影响

为阐明酸雨对早、晚稻叶片不同时期碳(C)、氮(N)、磷(P)含量及其生态化学计量学特征的影响,设置对照(Control,CK)、pH4.5、pH3.5酸雨处理,对福州沿江稻田早、晚稻叶片不同时期C、N、P含量及其生态化学计量学特征进行测定和分析。研究结果表明:早稻叶片C、N、P含量在拔节期和成熟期分别为(401.08±1.83)、(37.01±2.54)、(1.01±0.05) g/kg和(349.08±4.52)、(15.52±0.05)、(0.48±0.01) g/kg,晚稻C、N、P含量在拔节期和成熟期分别为(389.00±2.82)、(28.52±0.31)、(0.74±0.01) g/kg和(317.25±1.65)、(8.18±0.51)、(0.29±0.03) g/kg,早稻叶片养分含量整体显著高于晚稻(P0.05),且各处理拔节期养分含量均显著高于成熟期含量(P0.05),整体上,酸雨处理可显著降低早稻叶片在拔节期的C、N、P含量(P0.05)。早稻叶片C/N、C/P、N/P在拔节期和成熟期分别为(10.94±0.77)、(400.13±18.91)、(36.77±2.07)和(23.19±0.63)、(737.04±30.47)、(32.08±1.03),晚稻叶片C/N、C/P、N/P在拔节期和成熟期分别为(13.74±0.26)、(528.10±0.26)、(38.70±0.74)和(39.61±2.11)、(1148.97±103.82)、(28.90±1.27),整体上,晚稻叶片各项比值高于早稻,根据各处理之间叶片的N/P值发现,模拟酸雨并未改变水稻P限制现状,在水稻生长的过程中,尤其是在拔节期需要追施适量的磷肥。     

Nematode Fauna of Tropical Rainforest in Brazil: A Descriptive and Seasonal Approach

Studies of nematode assemblages in natural ecosystems can contribute to better understanding of the occurrence, relevance, and ecology of plant-parasitic and other soil nematodes. Nematode assemblages and environmental parameters (organic matter, water content (WC), bulk density (BD), total porosity (Po), soil respiration, and soil texture) were investigated in two seasons (rainy and dry) in two forest areas of the Zona da Mata, Pernambuco State. The aim of our research was to evaluate the heterogeneity between two locations and seasons in the Brazilian Atlantic Forest. Structure and composition of the nematode assemblages differed between areas and across time. Rhabditidae dominated the rainy season in both forest soils. Rarefaction curves (RC) suggest that sampling to detect more nematode taxa should be more intensive in the rainy season. The forest soils have complex, stable soil food webs with high connectance and decomposition channels dominated by bacteria. The predator–prey relationships were not affected by changes in soil properties that fluctuate with time.     

Disentangling the importance of ecological niches from stochastic processes across scales

Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity and composition. In contrast, more stochastic theories emphasize the importance of chance colonization, random extinction and ecological drift. The schisms between deterministic and stochastic perspectives, which date back to the earliest days of ecology, continue to fuel contemporary debates (e.g. niches versus neutrality). As illustrated by the pioneering studies of Robert H. MacArthur and co-workers, resolution to these debates requires consideration of how the importance of local processes changes across scales. Here, we develop a framework for disentangling the relative importance of deterministic and stochastic processes in generating site-to-site variation in species composition (β-diversity) along ecological gradients (disturbance, productivity and biotic interactions) and among biogeographic regions that differ in the size of the regional species pool. We illustrate how to discern the importance of deterministic processes using null-model approaches that explicitly account for local and regional factors that inherently create stochastic turnover. By embracing processes across scales, we can build a more synthetic framework for understanding how niches structure patterns of biodiversity in the face of stochastic processes that emerge from local and biogeographic factors.