Monitoring the impacts of anthropogenic threats and interventions to mitigate these threats is key to understanding how to best conserve biodiversity. Ecologists use many different study designs to ...monitor such impacts. Simpler designs lacking controls (e.g. Before–After (BA) and After) or pre‐impact data (e.g. Control–Impact (CI)) are considered to be less robust than more complex designs (e.g. Before–After Control‐Impact (BACI) or Randomized Controlled Trials (RCTs)). However, we lack quantitative estimates of how much less accurate simpler study designs are in ecology. Understanding this could help prioritize research and weight studies by their design's accuracy in meta‐analysis and evidence assessment.
We compared how accurately five study designs estimated the true effect of a simulated environmental impact that caused a step‐change response in a population's density. We derived empirical estimates of several simulation parameters from 47 ecological datasets to ensure our simulations were realistic. We measured design performance by determining the percentage of simulations where: (a) the true effect fell within the 95% Confidence Intervals of effect size estimates, and (b) each design correctly estimated the true effect's direction and magnitude. We also considered how sample size affected their performance.
We demonstrated that BACI designs performed: 1.3–1.8 times better than RCTs; 2.9–4.2 times versus BA; 3.2–4.6 times versus CI; and 7.1–10.1 times versus After designs (depending on sample size), when correctly estimating true effect's direction and magnitude to within ±30%. Although BACI designs suffered from low power at small sample sizes, they outperformed other designs for almost all performance measures. Increasing sample size improved BACI design accuracy, but only increased the precision of simpler designs around biased estimates.
Synthesis and applications. We suggest that more investment in more robust designs is needed in ecology since inferences from simpler designs, even with large sample sizes may be misleading. Facilitating this requires longer‐term funding and stronger research–practice partnerships. We also propose ‘accuracy weights’ and demonstrate how they can weight studies in three recent meta‐analyses by accounting for study design and sample size. We hope these help decision‐makers and meta‐analysts better account for study design when assessing evidence.
Foreign Language Japanese
生物多様性の保全を効果的に行うためには、人為的脅威の影響や保全対策の効果を適切に評価することが重要となる。生態学ではこのような評価を行うために、様々な研究デザインが用いられている。対照区が存在しないBefore‐After (BA)デザインやAfterデザイン、また処理以前のデータが存在しないControl‐Impact (CI)デザインなど簡素な研究デザインは、Before‐After Control‐Impact (BACI)デザインやランダム化比較試験（RCTs: Randomized Controlled Trials)などの複雑なデザインよりも頑健さに劣ると考えられている。しかしながら、生態学においてこれら簡素な研究デザインがどれだけ正確度に劣るのか、定量的な評価はこれまで行われていない。研究デザインの正確度を定量的に評価することで、メタ解析やエビデンスの評価を行う際に、用いられた研究デザインの正確度に基づいて各研究の優先順位付けや重み付けを行うことが可能になるだろう。
本研究では、環境変化が個体群密度に及ぼす影響を、5種類の研究デザインがどれだけ正確に推定することができるのか、シミュレーションを用いて検討した。より現実に即した状況を再現するため、シミュレーションで用いたパラメータは、47の生態学的データから抽出した。各研究デザインの正確度は、シミュレーションにおいて、（１）推定された効果サイズの95％信頼区間に真の効果が含まれる割合、（２）推定された効果が真の効果の方向・程度と一致した割合、を算出することによって評価した。またサンプルサイズの違いが各研究デザインの正確度に及ぼす影響も検討した。
シミュレーションの結果、BACIデザインはランダム化比較試験に対して1.3–1.8倍、BAデザインに対して2.9–4.2倍、CIデザインに対して3.2–4.6倍、Afterデザインに比較すると7.1–10.1倍も正確に真の効果を推定できる（推定された効果が真の効果の方向と一致し、且つ真の効果の ± 30%内に含まれる）ことが明らかになった（比較値のばらつきはサンプルサイズによる）。BACIデザインの正確度はサンプルサイズが小さい場合には低下したが、それでもほとんどの指標において他のデザインよりも高い正確度を示していた。サンプルサイズを増やすことでBACIデザインの正確度は向上したが、他の研究デザインでは偏った推定値の精度が向上するだけであった。
Synthesis and applications. 例えサンプルサイズが十分であったとしても、簡素なデザインに基づいた推論は正確でない可能性があるため、生態学においてもより頑健な研究デザインの利用を推進していく必要があると考えられる。頑健な研究デザインの利用を推進するためには、長期に渡る研究資金の確保や、研究と実践の間でのより強固な連携が必要となるだろう。本研究では更にこれらの結果に基づいて、メタ解析において研究デザインとサンプルサイズに基づいて各研究の重み付けをする手法を提案し、近年行われた３つのメタ解析を用いてその実用例を提示した。これらの結果は、意思決定者やメタ解析を行う研究者が、研究デザインを考慮したエビデンスの評価を行うために有用となるだろう。
We suggest that more investment in more robust designs is needed in ecology since inferences from simpler designs, even with large sample sizes may be misleading. Facilitating this requires longer‐term funding and stronger research–practice partnerships. We also propose ‘accuracy weights’ and demonstrate how they can weight studies in three recent meta‐analyses by accounting for study design and sample size. We hope these help decision‐makers and meta‐analysts better account for study design when assessing evidence.
Evaluating Impact Using Time-Series Data Wauchope, Hannah S.; Amano, Tatsuya; Geldmann, Jonas ...
Trends in ecology & evolution (Amsterdam),
March 2021, 2021-03-00, Letnik:
36, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Humanity’s impact on the environment is increasing, as are strategies to conserve biodiversity, but a lack of understanding about how interventions affect ecological and conservation outcomes hampers ...decision-making. Time series are often used to assess impacts, but ecologists tend to compare average values from before to after an impact; overlooking the potential for the intervention to elicit a change in trend. Without methods that allow for a range of responses, erroneous conclusions can be drawn, especially for large, multi-time-series datasets, which are increasingly available. Drawing on literature in other disciplines and pioneering work in ecology, we present a standardised framework to robustly assesses how interventions, like natural disasters or conservation policies, affect ecological time series.
Ecologists have called for more robust studies on the impact of conservation interventions, or environmental shocks, on outcomes of interest, such as populations, habitat loss, or pressures.Time-series data are increasingly available and can, if appropriately analysed, allow such causal inferences.However, there are important pitfalls that make large-scale analyses involving multiple time series problematic.There has been progress in a range of fields, but the literature is fragmented and not all is easily accessible to ecologists.A framework is presented, with clear and consistent terminology, to support ecologists to conduct effective impact evaluation with time-series data. This will allow them to contribute to better-informed environmental management decisions.
A ubiquitous pattern in ecological systems is that more abundant species tend to be more generalist; that is, they interact with more species or can occur in wider range of habitats. However, there ...is no consensus on whether generalism drives abundance (a selection process) or abundance drives generalism (a drift process). As it is difficult to conduct direct experiments to solve this chicken-and-egg dilemma, previous studies have used a causal discovery method based on formal logic and have found that abundance drives generalism. Here, we refine this method by correcting its bias regarding skewed distributions, and employ two other independent causal discovery methods based on nonparametric regression and on information theory, respectively. Contrary to previous work, all three independent methods strongly indicate that generalism drives abundance when applied to datasets on plant-hummingbird communities and reef fishes. Furthermore, we find that selection processes are more important than drift processes in structuring multispecies systems when the environment is variable. Our results showcase the power of the computational causal discovery approach to aid ecological research.
The challenge of biased evidence in conservation Christie, Alec P.; Amano, Tatsuya; Martin, Philip A. ...
Conservation biology,
February 2021, 2021-02-00, 20210201, Letnik:
35, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Efforts to tackle the current biodiversity crisis need to be as efficient and effective as possible given chronic underfunding. To inform decision‐makers of the most effective conservation actions, ...it is important to identify biases and gaps in the conservation literature to prioritize future evidence generation. We used the Conservation Evidence database to assess the state of the global literature that tests conservation actions for amphibians and birds. For the studies in the database, we investigated their spatial and taxonomic extent and distribution across biomes, effectiveness metrics, and study designs. Studies were heavily concentrated in Western Europe and North America for birds and particularly for amphibians, and temperate forest and grassland biomes were highly represented relative to their percentage of land coverage. Studies that used the most reliable study designs—before‐after control‐impact and randomized controlled trials—were the most geographically restricted and scarce in the evidence base. There were negative spatial relationships between the numbers of studies and the numbers of threatened and data‐deficient species worldwide. Taxonomic biases and gaps were apparent for amphibians and birds—some entire orders were absent from the evidence base—whereas others were poorly represented relative to the proportion of threatened species they contained. Metrics used to evaluate effectiveness of conservation actions were often inconsistent between studies, potentially making them less directly comparable and evidence synthesis more difficult. Testing conservation actions on threatened species outside Western Europe, North America, and Australasia should be prioritized. Standardizing metrics and improving the rigor of study designs used to test conservation actions would also improve the quality of the evidence base for synthesis and decision‐making.
El Desafío de la Evidencia Sesgada en la Conservación
Resumen
Los esfuerzos para lidiar con la actual crisis de la biodiversidad necesitan ser tan eficientes y efectivos como sea posible dado el crónico subfinanciamiento. Para informar a los órganos de decisión sobre las acciones de conservación más efectivas, es importante identificar los sesgos y las brechas en la literatura de la conservación para priorizar generación de evidencias en el futuro. Usamos la base de datos Conservation Evidence para evaluar el estado de la literatura mundial que analiza las acciones para la conservación de anfibios y aves. Para los estudios dentro de la base de datos, investigamos su extensión espacial y taxonómica y su distribución a lo largo de biomas, medidas de efectividad y diseños de estudio. Los estudios se concentraron principalmente en Europa Occidental y en América del Norte en el caso de las aves y particularmente para los anfibios. Los biomas con mayor representación en relación con su porcentaje de cobertura de suelo fueron el bosque templado y los pastizales. Los estudios que utilizaron el diseño más confiable ‐ impacto del control antes‐ después y ensayos controlados al azar ‐ fueron los que presentaron mayor restricción geográfica y menor presencia dentro de la base de evidencias. También encontramos relaciones espaciales negativas entre el número de estudios y el número de especies amenazadas o con pocos datos a nivel mundial. Los sesgos y las brechas taxonómicas fueron evidentes para los anfibios y las aves ‐ hubo órdenes enteros ausentes en la base de evidencias ‐ mientras que otros taxones estuvieron representados pobremente en relación con la proporción de especies amenazadas que albergan. Las medidas utilizadas para evaluar la efectividad de las acciones de conservación con frecuencia fueron incompatibles entre los estudios, lo que las hace potencialmente menos comparables directamente y también dificulta la síntesis de las evidencias. Se debe priorizar el análisis de las acciones para la conservación de las especies que se encuentran fuera de Europa Occidental, América del Norte y Australasia. La estandarización de las medidas y el mejoramiento del rigor de los diseños de estudio que se usan para evaluar las acciones de conservación también mejoraría la calidad de la base de evidencias para la síntesis y la toma de decisiones.
摘要
鉴于生物多样性保护长期面临着资金不足问题, 应对当下生物多样性危机的努力必须尽可能高效和有用。为了让决策者了解最有效的保护行动, 分辨保护文献中的偏倚和空缺来优先进行未来收集保护证据的工作十分重要。我们用保护证据数据库评估了全球两栖动物和鸟类保护行动的研究文献的情况, 并分析了数据库中研究的生物群系在空间和分类学上的范围和分布、有效性指标和研究设计。鸟类的研究主要集中在西欧和北美, 两栖动物也尤其如此, 另外, 对温带森林和草原的生物群系的研究相对于它们在陆地上的覆盖率有很高的代表性。采用最可靠的前后对照影响分析和随机对照试验设计的研究最容易受到地域限制且证据基础最少。全世界范围内, 研究数量与受威胁和缺乏数据的物种数量在空间上存在负相关关系。两栖动物和鸟类明显存在分类学偏倚和研究空缺, 有些目完全没有证据基础, 还有一些目相对于它们所包含的濒危物种的比例来说没有得到足够代表。此外, 用于评估保护行动有效性的指标在研究之间常常不一致, 可能导致研究不能直接比较, 而且证据的综合更加困难。我们提出, 应优先对西欧、北美和澳大拉西亚以外的濒危物种的保护行动进行调查。指标标准化、提高用于检验保护行动有效性研究设计的严谨性, 也将提高用于综合分析和决策的证据基础的质量。翻译: 胡怡思; 审校: 聂永刚
Article impact statement: Severe taxonomic and geographic biases threaten evidence‐based conservation efforts.
Indirect interactions play an essential role in governing population, community and coevolutionary dynamics across a diverse range of ecological communities. Such communities are widely represented ...as bipartite networks: graphs depicting interactions between two groups of species, such as plants and pollinators or hosts and parasites. For over thirty years, studies have used indices, such as connectance and species degree, to characterise the structure of these networks and the roles of their constituent species. However, compressing a complex network into a single metric necessarily discards large amounts of information about indirect interactions. Given the large literature demonstrating the importance and ubiquity of indirect effects, many studies of network structure are likely missing a substantial piece of the ecological puzzle. Here we use the emerging concept of bipartite motifs to outline a new framework for bipartite networks that incorporates indirect interactions. While this framework is a significant departure from the current way of thinking about bipartite ecological networks, we show that this shift is supported by analyses of simulated and empirical data. We use simulations to show how consideration of indirect interactions can highlight differences missed by the current index paradigm that may be ecologically important. We extend this finding to empirical plant–pollinator communities, showing how two bee species, with similar direct interactions, differ in how specialised their competitors are. These examples underscore the need to not rely solely on network‐ and species‐level indices for characterising the structure of bipartite ecological networks.
As mobile genetic elements, plasmids are central for our understanding of antimicrobial resistance spread in microbial communities. Plasmids can have varying fitness effects on their host bacteria, ...which will markedly impact their role as antimicrobial resistance vectors. Using a plasmid population model, we first show that beneficial plasmids interact with a higher number of hosts than costly plasmids when embedded in a community with multiple hosts and plasmids. We then analyse the network of a natural host-plasmid wastewater community from a Hi-C metagenomics dataset. As predicted by the model, we find that antimicrobial resistance encoding plasmids, which are likely to have positive fitness effects on their hosts in wastewater, interact with more bacterial taxa than non-antimicrobial resistance plasmids and are disproportionally important for connecting the entire network compared to non- antimicrobial resistance plasmids. This highlights the role of antimicrobials in restructuring host-plasmid networks by increasing the benefits of antimicrobial resistance carrying plasmids, which can have consequences for the spread of antimicrobial resistance genes through microbial networks. Furthermore, that antimicrobial resistance encoding plasmids are associated with a broader range of hosts implies that they will be more robust to turnover of bacterial strains.
Nestedness is a widespread pattern in mutualistic networks that has high ecological and evolutionary importance due to its role in enhancing species persistence and community stability. Nestedness ...measures tend to be correlated with fundamental properties of networks, such as size and connectance, and so nestedness values must be normalised to enable fair comparisons between different ecological communities. Current approaches, such as using null‐corrected nestedness values and z‐scores, suffer from extensive statistical issues. Thus a new approach called NODFc was recently proposed, where nestedness is expressed relative to network size, connectance and the maximum nestedness that could be achieved in a particular network. While this approach is demonstrably effective in overcoming the issues of collinearity with basic network properties, it is computationally intensive to calculate, and current approaches are too slow to be practical for many types of analysis, or for analysing large networks.
We developed three highly optimised algorithms, based on greedy, hill climbing and simulated annealing approaches, for calculation of NODFc, spread along a speed‐quality continuum. Users thus have the choice between a fast algorithm with a less accurate estimate, a slower algorithm with a more accurate estimate and an intermediate option.
We outline the package and its implementation, as well as provide comparative performance benchmarking and two example analyses. We show that maxnodf enables speed increases of hundreds of times faster than existing approaches, with large networks seeing the biggest improvements. For example, for a large network with 3,000 links, computation time was reduced from 50 min using the fastest existing algorithm to 11 s using maxnodf.
maxnodf makes correctly normalised nestedness measures feasible for complex analyses of even large networks. Analyses that would previously take weeks to complete can now be finished in hours or even seconds. Given evidence that correctly normalising nestedness values can significantly change the conclusions of ecological studies, we believe this package will usher in necessary widespread use of appropriate comparative nestedness statistics.
International policy is focused on increasing the proportion of the Earth's surface that is protected for nature
. Although studies show that protected areas prevent habitat loss
, there is a lack of ...evidence for their effect on species' populations: existing studies are at local scale or use simple designs that lack appropriate controls
. Here we explore how 1,506 protected areas have affected the trajectories of 27,055 waterbird populations across the globe using a robust before-after control-intervention study design, which compares protected and unprotected populations in the years before and after protection. We show that the simpler study designs typically used to assess protected area effectiveness (before-after or control-intervention) incorrectly estimate effects for 37-50% of populations-for instance misclassifying positively impacted populations as negatively impacted, and vice versa. Using our robust study design, we find that protected areas have a mixed impact on waterbirds, with a strong signal that areas managed for waterbirds or their habitat are more likely to benefit populations, and a weak signal that larger areas are more beneficial than smaller ones. Calls to conserve 30% of the Earth's surface by 2030 are gathering pace
, but we show that protection alone does not guarantee good biodiversity outcomes. As countries gather to agree the new Global Biodiversity Framework, targets must focus on creating and supporting well-managed protected and conserved areas that measurably benefit populations.
Interactions between species generate the functions on which ecosystems and humans depend. However, we lack an understanding of the risk that interaction loss poses to ecological communities. Here, ...we quantify the risk of interaction loss for 4,330 species interactions from 41 empirical pollination and seed dispersal networks across 6 continents. We estimate risk as a function of interaction vulnerability to extinction (likelihood of loss) and contribution to network feasibility, a measure of how much an interaction helps a community tolerate environmental perturbations. Remarkably, we find that more vulnerable interactions have higher contributions to network feasibility. Furthermore, interactions tend to have more similar vulnerability and contribution to feasibility across networks than expected by chance, suggesting that vulnerability and feasibility contribution may be intrinsic properties of interactions, rather than only a function of ecological context. These results may provide a starting point for prioritising interactions for conservation in species interaction networks in the future.
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