Quantitatively Evaluating Restoration Experiments: Research Design, Statistical Analysis, and Data Management Considerations

Conceptual and logistical challenges associated with the design and analysis of ecological restoration experiments are often viewed as being insurmountable, thereby limiting the potential value of restoration experiments as tests of ecological theory. Such research constraints are, however, not unique within the environmental sciences. Numerous natural and anthropogenic disturbances represent unplanned, uncontrollable events that cannot be replicated or studied using traditional experimental approaches and statistical analyses. A broad mix of appropriate research approaches (e.g., long-term studies, large-scale comparative studies, space-for-time substitution, modeling, and focused experimentation) and analytical tools (e.g., observational, spatial, and temporal statistics) are available and required to advance restoration ecology as a scientific discipline. In this article, research design and analytical options are described and assessed in relation to their applicability to restoration ecology. Significant research benefits may be derived from explicitly defining conceptual models and presuppositions, developing multiple working hypotheses, and developing and archiving high-quality data and metadata. Flexibility in research approaches and statistical analyses, high-quality databases, and new sampling approaches that support research at broader spatial and temporal scales are critical for enhancing ecological understanding and supporting further development of restoration ecology as a scientific discipline.     

Biology student teachers’ dialogic talk in inquiry-based instruction

ABSTRACT

Inquiry-based learning has generally accepted by scholars as a most effective teaching approach in biology education. The talk during inquiry-based teaching needs to be practiced. There is less evidence how student teachers talk with students during their inquiry-based biology instruction. This knowledge is needed in supporting student teachers to develop their teachership in biology education. In this qualitative case study, the dialogic talk of biology student teachers (N = 6) was studied in the context of inquiry-based lessons in lower secondary school. The student teachers’ lessons were video and audio recorded and the data was analyzed using content analysis. The student teachers used dialogic talk in their inquiry-based instruction only occasionally, mainly in the examination and the conclusion stages. During the introduction stage, dialogic talk was less used and it was mainly explaining and instructing the content. In the examination stage, student teachers also guided students and stated facts. During the conclusion stage, student teachers mainly explained and also evaluated students’ statements. The lesson’s topics and methods used in inquiry-based learning may enable the dialogic talk of student teacher to some extent. However, teacher education should focus more on scaffolding student teachers’ talk with their students in all kinds of inquiry approaches.     

Phylogeny, ecology, and the coupling of comparative and experimental approaches

Recent progress in the development of phylogenetic methods and access to molecular phylogenies has made comparative biology more popular than ever before. However, determining cause and effect in phylogenetic comparative studies is inherently difficult without experimentation and evolutionary replication. Here, we provide a roadmap for linking comparative phylogenetic patterns with ecological experiments to test causal hypotheses across ecological and evolutionary scales. As examples, we consider five cornerstones of ecological and evolutionary research: tests of adaptation, tradeoffs and synergisms among traits, coevolution due to species interactions, trait influences on lineage diversification, and community assembly and composition. Although several scenarios can result in a lack of concordance between historical patterns and contemporary experiments, we argue that the coupling of phylogenetic and experimental methods is an increasingly revealing approach to hypothesis testing in evolutionary ecology.     

Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change—A review

Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy‐making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain process‐oriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science‐based policy formulation.     

Gene expression profiling: opening the black box of plant ecosystem responses to global change

The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Because the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical, and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and nonmodel species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.     

Contingent Conclusions: Year of Initiation Influences Ecological Field Experiments,but Temporal Replication is Rare

Interannual variation in experimental field conditions produce variability in the results of experiments monitored over multiple years, termed here “year effects.” When experimental treatments are replicated in separate years, interannual variation may influence treatment effects and produce significant treatment by initiation‐year interactions. Understanding the frequency and strength of these effects requires initiating identical experiments across years. We conducted a review of literature covering more than 500 experimental articles published in 7 journals between 1966 and 2008. Only 5% of the 276 general ecological field studies initiated experiments in multiple years. This rarity was even more evident in the journal Restoration Ecology, in which none of the 173 surveyed experimental studies initiated experiments in multiple years. In contrast, 48% of the 58 field experiments published in an agronomy journal were replicated across years. We found only 17 studies that tested treatment by initiation‐year interactions. Despite their rarity, 76% of these studies found significant interactions between treatment and initiation year. We conclude that the results of many ecological field experiments are likely to be contingent on the year in which they are implemented. We discuss the importance of treatment by initiation‐year interactions in ecology and restoration, factors that have hindered the inclusion of temporal replication in the past, and some suggestions for the appropriate design and analysis of temporally replicated experiments. We argue for more deliberate investigation of temporal contingency in ecological experimentation, especially in the field of restoration ecology, which may be particularly sensitive to treatment by initiation‐year interactions.     

Mechanistic analogy: how microcosms explain nature

Microcosm studies of ecological processes have been criticized for being unrealistic. However, since lack of realism is inherent to all experimental science, if lack of realism invalidates microcosm models of ecological processes, then such lack of realism must either also invalidate much of the rest of experimental ecology or its force with respect to microcosm studies must derive from some other limitation of microcosm apparatus. We believe that the logic of the microcosm program for ecological research has been misunderstood. Here, we respond to the criticism that microcosm studies play at most a heuristic role in ecology with a new account of scientific experimentation developed specifically with ecology and other environmental sciences in mind. Central to our account are the concepts of model-based reasoning and analogical inference. We find that microcosm studies are sound when they serve as models for nature and when certain properties, referred to as the essential properties, are in positive analogy. By extension, our account also justifies numerous other kinds of ecological experimentation. These results are important because reliable causal accounts of ecological processes are necessary for sound application of ecological theory to conservation and environmental science. A severe sensitivity to reliable representation of causes is the chief virtue of the microcosm approach.     

合成微生物体系研究进展

合成微生物体系作为自下而上构建的人工合成微生物群落,相比于自然微生物群落具有复杂度低及可控性、可操作性强等特点。其作为新兴的生物技术,综合借鉴了合成生物学、系统生物学、生物进化等知识,通过合理的设计、规划与调控,成为研究微生物生态学理论的实验平台,以及验证已知理论的微生物系统。本文首先简单介绍了合成微生物体系的概念及其由来,阐述了其基本构建原则,随后介绍了其生态学理论基础,并总结概括了近年来的实际应用,最后提出合成微生物体系的发展前景,包括需要设计构建更为复杂的人工合成微生物群落,以及优化生态模型。     

Make biology relevant again! Pre-service teachers’ views on the relevance of biology education

ABSTRACT

Biology education should be relevant to young students so that they can become interested in biology and understand biological topics in their everyday and vocational lives. We conducted interviews and collected mind maps to examine Finnish pre-service biology teachers’ (N = 16) views on the relevance of biology education. Furthermore, we analysed Finnish secondary school biology curricula, which were compared with the pre-service teachers’ answers. We classified the views on relevance into nine main categories using grounded theory as the methodological frame of reference. Pre-service teachers emphasised the relevance of biology to the student’s own life, whereas scientific practices and the nature of science were expressed in secondary school curricula more often. Novice pre-service teachers put more value on general knowledge, while more experienced pre-service teachers were more likely to mention sustainable futures and societal aspects in their reasoning. Based on the results, we identified two stages in the development of the views. This study suggests that pedagogical studies, teaching experience and teacher training have an impact on the pre-service teachers’ views about the relevance of biology education. Moreover, we could find differences between curricula and pre-service teachers’ views, especially regarding scientific practices and the role of the nature of science in biology education.     

Molecular approaches for AM fungal community ecology: A primer

Molecular techniques are no longer optional for ecologists interested in arbuscular mycorrhizal (AM) communities. Understanding the role of these soil fungi in natural systems requires knowledge of their abundance and identity but this is impossible to achieve without a molecular approach. Adapting molecular tools to AM fungi can be challenging because of the unique biology of the fungi. Moreover, many recruits in the field of mycorrhizal ecology have little or no experience with molecular biology. Here, we outline a conceptual framework for designing robust ecological experiments with AM fungi using molecular approaches.     

Ecological engineering: A rationale for standardized curriculum and professional certification in the United States

The demand for engineering solutions to ecosystem–level problems has increased as the impact of human activities has expanded to global proportions. While the science of restoration ecology has been developed to address many critical ecosystem management issues, the high degree of complexity and uncertainty associated with these issues demands a more quantitative approach. Ecological engineering uses science-based quantification of ecological processes to develop and apply engineering-based design criteria for sustainable systems. We suggest that in the United States ecological engineering curricula should be offered at the graduate level and should require rigorous Accreditation Board of Engineering and Technology-accredited (or equivalent) undergraduate preparation in engineering fundamentals. In addition to strengthening students’ mastery of engineering theory and application, the graduate curriculum should provide core courses in ecosystem theory including quantitative ecology, systems ecology, restoration ecology, ecological engineering, ecological modeling, and ecological engineering economics. Advanced courses in limnology, environmental plant physiology, ecological economics, and specific ecosystem design should be provided to address students’ specific professional objectives. Finally, professional engineering certification must be developed to insure the credibility of this new engineering specialization.     

A case for project based learning to enact semantic waves: towards cumulative knowledge building

ABSTRACT

First-year undergraduate curricula and their delivery should assist students in the transition from previous learning experiences to learning in higher education. However, the so-called articulation gap or discontinuity between secondary and higher education has been identified as a key structural curriculum problem for first-year success in South Africa and abroad. Valuable insights into this problem came from a recent study that drew on Legitimation Code Theory (LCT). Findings revealed an unexpectedly wide gap between the high school and the university biology curricula. The high school biology curriculum displays minimal movement between context-dependent, simpler meaning and relatively decontextualized, condensed meaning common in first-year biology. LCT Semantics was also found to be a valuable tool for restructuring curricula and pedagogy to intentionally enact semantic movement and thereby a more gradual transition for students from high school to university. This paper reports on an integrative first-year biology project aimed intentionally at taking students’ concept knowledge through a wide contextual range, and repeatedly between less and more complex meaning. I reflect on how the project design steers students towards creating semantic movement during their presentations, thereby contributing to cumulative knowledge building and a more gradual transition towards first-year epistemological access.     

An "enactive" approach to integrative and comparative biology: thoughts on the table

We discuss the concept of Enaction as originally proposed by Varela. We attempt to exemplify through two specific topics, sensory ecology and behavior, as well as physiological and behavioral ecology, on which the enactive approach is based. We argue that sensory physiology allows us to explore the biological and cognitive meaning of animal 'private' sensory channels, beyond the scope of our own sensory capacity. Furthermore, after analyzing the interplay between factors that may impose limits upon an animal's use of time and energy, we call for a program of research in integrative and comparative biology that simultaneously considers evolutionary ecology (including physiological and behavioral ecology) and neurobiology (including cognitive mechanisms as well structural design). We believe that this approach represents a shift in scientific attitude among biologists concerning the place of biological and ecological topics in studies of integrative and comparative biology and biological diversity and vice versa.     

Engineering microbial systems to explore ecological and evolutionary dynamics

A major goal of biological research is to provide a mechanistic understanding of diverse biological processes. To this end, synthetic biology offers a powerful approach, whereby biological questions can be addressed in a well-defined framework. By constructing simple gene circuits, such studies have generated new insights into the design principles of gene regulatory networks. Recently, this strategy has been applied to analyze ecological and evolutionary questions, where population-level interactions are critical. Here, we highlight recent development of such systems and discuss how they were used to address problems in ecology and evolutionary biology. As illustrated by these examples, synthetic ecosystems provide a unique platform to study ecological and evolutionary phenomena that are challenging to study in their natural contexts.     

Fishing for an ECG: a student-directed electrocardiographic laboratory using rainbow trout

Cardiac physiology is emphasized in many undergraduate physiology courses, but few nonmammalian vertebrate model systems exist that 1) can be studied fairly noninvasively, 2) are well suited for controlled experimentation, and 3) emphasize principles characteristic of the vertebrate heart. We have developed an inquiry-based undergraduate/graduate-level laboratory in cardiac physiology and electrocardiography using rainbow trout (Oncorhynchus mykiss Walbaum) and the BioPac MP30 data-acquisition system (other fish species and/or electrocardiographic recording devices can be substituted). This laboratory facilitates intensive study of vertebrate electrocardiograms (ECGs) under a variety of environmental and physiological perturbations and is ideal for use in multi-session, inquiry-based laboratory projects in animal physiology. Furthermore, students gain valuable experience in scientific inquiry, study design, following and/or developing scientific protocols, and animal care. This laboratory requires the ability to keep captive fish of at least 100 g and equipment to record ECGs. Departments meeting these requirements can adopt this technique at modest expense. Student enthusiasm and feedback were positive, and several students commented that the nonlethal methods used added to the laboratory's perceived value.     

如何写好数据分析和几个相关的统计问题

该文就生态学论文“材料和方法”部分中“数据分析”的写作规范进行讨论, 希望对论文写作有所帮助。还讨论了在生态学论文数据分析部分常遇到的几个统计问题, 如采用更有效的统计方法、相关因变量、方差不齐性、统计显著性与生物学/生态学显著性、伪重复问题。     

A review of the use of the brine shrimp,Artemia spp,for teaching practical biology in schools and colleges

Brine shrimps are salt water Crustacea that are cheaply, easily, and rapidly reared in schools. In several studies they have proved to be attractive to pupils and valuable for teaching ecology and animal behaviour. Using simple and inexpensive apparatus such as plastic bottles, pipettes, sieves, and magnifiers pupils may investigate their feeding, growth, and development, observe reproductive behaviour and, by means of planned investigations, learn important lessons in animal ecology. Brine shrimps have a demonstrated usefulness for teaching and learning at every level of education — from primary, through secondary science, to undergraduate biology project work. In school, brine shrimps present fewer ethical problems than those posed by the keeping of many other laboratory animals, yet at the same time give opportunity for ethical discussion. The extensive utilitarian use of brine shrimps in research and fisheries may provide a technical and commercial link to classroom science.     

Rethinking the common garden in invasion research

In common garden experiments, a number of genotypes are raised in a common environment in order to quantify the genetic component of phenotypic variation. Common gardens are thus ideally suited for disentangling how genetic and environmental factors contribute to the success of invasive species in their new non-native range. Although common garden experiments are increasingly employed in the study of invasive species, there has been little discussion about how these experiments should be designed for greatest utility. We argue that this has delayed progress in developing a general theory of invasion biology. We suggest a minimum optimal design (MOD) for common garden studies that target the ecological and evolutionary processes leading to phenotypic differentiation between native and invasive ranges. This involves four elements: (A) multiple, strategically sited garden locations, involving at the very least four gardens (2 in the native range and 2 in the invaded range); (B) careful consideration of the genetic design of the experiment; (C) standardization of experimental protocols across all gardens; and (D) care to ensure the biosafety of the experiment. Our understanding of the evolutionary ecology of biological invasions will be greatly enhanced by common garden studies, if and only if they are designed in a more systematic fashion, incorporating at the very least the MOD suggested here.     

Student‐led field studies of herbivory: Hands‐on experiences for remote (or in‐person) learning

Challenging students to independently design and implement experiments is a powerful way to teach the scientific method while engaging with STEM‐related course material. For ecology and organismal biology, such experiences often take the form of field work. The COVID‐19 pandemic presented formidable challenges for instructors of such courses: How can students conduct any experiments, much less ones of their own design, when they might not even have access to campus? Here we describe a student‐led field project exploring invertebrate herbivory in terrestrial plant systems. Designed to flexibly accommodate student groups working either in‐person, remotely, or both, the project would be suitable for invertebrate biology, plant biology, or general ecology courses at the college or high school level. We describe our implementation in two sections of a sophomore‐level course, provide specific advice based on our experiences, make suggestions for future improvements or adaptations, and provide all the written materials that instructors would need to implement this in their own teaching.     

Phytochemical diversity and synergistic effects on herbivores

Synergistic effects of multiple plant secondary metabolites on upper trophic levels constitute an underexplored but potentially widespread component of coevolution and ecological interactions. Examples of plant secondary metabolites acting synergistically as insect deterrents are not common, and many studies focus on the pharmaceutical applications of natural products, where activity is serendipitous and not an evolved response. This review summarizes some systems that are ideal for testing synergistic plant defenses and utilizes a focused meta-analysis to examine studies that have tested effects of multiple compounds on insects. Due to a dearth of ecological synergy studies, one of the few patterns for synergy that we are able to report from the meta-analysis is that phytochemical mixtures have a larger overall effect on generalist herbivores than specialist herbivores. We recommend a focus on synergy in chemical ecology programs and suggest future hypothesis tests and methods. These approaches are not focused on techniques in molecular biology to examine mechanisms at the cellular level, rather we recommend uncovering the existence of synergy first, by combining the best methods in organic synthesis, isolation, chemical ecology, bioassays, and quantitative analyses. Data generated by our recommended methods should provide rigorous tests of important hypotheses on how intraclass and interclass compounds act synergistically to deter insects, disrupt the immune response, and ultimately contribute to diversification. Further synergy research should also contribute to determining if antiherbivore synergy is widespread among plant secondary metabolites, which would be consistent with the hypothesis that synergistic defenses are a key attribute of the evolved diverse chemical mixtures found in plants.