The Hierarchy-of-Hypotheses Approach: A Synthesis Method for Enhancing Theory Development in Ecology and Evolution.
Ontology highlight
ABSTRACT:
SUBMITTER: Heger T
PROVIDER: S-EPMC8038874 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Research hypotheses have been a cornerstone of science since before Galileo. Many have argued that hypotheses (1) encourage discovery of mechanisms, and (2) reduce bias-both features that should increase transferability and reproducibility. However, we are entering a new era of big data and highly predictive models where some argue the hypothesis is outmoded. We hypothesized that hypothesis use has declined in ecology and evolution since the 1990s, given the substantial advancement of tools further facilitating descriptive, correlative research. Alternatively, hypothesis use may have become more frequent due to the strong recommendation by some journals and funding agencies that submissions have hypothesis statements. Using a detailed literature analysis (N = 268 articles), we found prevalence of hypotheses in eco-evo research is very low (6.7%-26%) and static from 1990-2015, a pattern mirrored in an extensive literature search (N = 302,558 articles). Our literature review also indicates that neither grant success nor citation rates were related to the inclusion of hypotheses, which may provide disincentive for hypothesis formulation. Here, we review common justifications for avoiding hypotheses and present new arguments based on benefits to the individual researcher. We argue that stating multiple alternative hypotheses increases research clarity and precision, and is more likely to address the mechanisms for observed patterns in nature. Although hypotheses are not always necessary, we expect their continued and increased use will help our fields move toward greater understanding, reproducibility, prediction, and effective conservation of nature.
| S-EPMC8207363 | biostudies-literature
Project description:Science provides a method to learn about the relationships between observed patterns and the processes that generate them. However, inference can be confounded when an observed pattern cannot be clearly and wholly attributed to a hypothesized process. Over-reliance on traditional single-hypothesis methods (i.e. null hypothesis significance testing) has resulted in replication crises in several disciplines, and ecology exhibits features common to these fields (e.g. low-power study designs, questionable research practices, etc.). Considering multiple working hypotheses in combination with pre-data collection modelling can be an effective means to mitigate many of these problems. We present a framework for explicitly modelling systems in which relevant processes are commonly omitted, overlooked or not considered and provide a formal workflow for a pre-data collection analysis of multiple candidate hypotheses. We advocate for and suggest ways that pre-data collection modelling can be combined with consideration of multiple working hypotheses to improve the efficiency and accuracy of research in ecology.
| S-EPMC7353960 | biostudies-literature
Project description:The use of multiple working hypotheses to gain strong inference is widely promoted as a means to enhance the effectiveness of scientific investigation. Only 21 of 100 randomly selected studies from the ecological and evolutionary literature tested more than one hypothesis and only eight tested more than two hypotheses. The surprising rarity of application of multiple working hypotheses suggests that this gap between theory and practice might reflect some fundamental issues. Here, we identify several intellectual and practical barriers that discourage us from using multiple hypotheses in our scientific investigation. While scientists have developed a number of ways to avoid biases, such as the use of double-blind controls, we suspect that few scientists are fully aware of the potential influence of cognitive bias on their decisions and they have not yet adopted many techniques available to overcome intellectual and practical barriers in order to improve scientific investigation.
| S-EPMC5319344 | biostudies-literature
Project description:The diets of Australopithecus africanus and Paranthropus robustus are hypothesized to have included C4 plants, such as tropical grasses and sedges, or the tissues of animals which themselves consumed C4 plants. Yet inferences based on the craniodental morphology of A. africanus and P. robustus indicate a seasonal diet governed by hard, brittle foods. Such mechanical characteristics are incompatible with a diet of grasses or uncooked meat, which are too tough for efficient mastication by flat, low-cusped molars. This discrepancy, termed the C4 conundrum, has led to the speculation that C4 plant underground storage organs (USOs) were a source of nutrition for hominin species. We test this hypothesis by examining the isotopic ecology of African mole rats, which consume USOs extensively. We measured delta18O and delta13C of enamel and bone apatite from fossil and modern species distributed across a range of habitats. We show that delta18O values vary little and that delta13C values vary along the C3 to C4/CAM-vegetative axis. Relatively high delta13C values exist in modern Cryptomys hottentotus natalensis and Cryptomys spp. recovered from hominin-bearing deposits. These values overlap those reported for A. africanus and P. robustus and we conclude that the USO hypothesis for hominin diets retains certain plausibility.
| S-EPMC2493578 | biostudies-literature
Project description:The phenomenon of cancer cell heterogeneity has been explained by different hypotheses, each entailing different therapy strategies. The most recent is the cancer stem cell model, which says that tumourigenicity and self-renewal are restricted to rare stem cell-like cancer cells. Since its conception, conflicting evidence has been published. In this study, we tested the applicability of a new approach developed in the field of ecology, the hierarchy-of-hypotheses approach, for the Cancer Stem Cell hypothesis. This approach allows to structure a broad concept into more specific sub-hypotheses, which in turn can be connected to available empirical studies. To generate a dataset with empirical studies, we conducted a systematic literature review in the Web of Science limited to the first 1000 publications returned by the search. From this pool, 51 publications were identified that tested whether a cell sub-population had cancer stem cell properties. By classifying the studies according to: (1) assessed indicators, (2) experimental assays and (3) model cancer cells used, we built a hierarchical structure of sub-hypotheses. The empirical tests from the selected studies were subsequently assigned to this hierarchy of hypotheses, and the percentage of supporting, undecided and questioning evidence was calculated for each sub-hypothesis, as well as additional experimental characteristics. Our approach successfully allowed us to determine that within our dataset, the empirical support for the CSC hypothesis was only 49.0%. The support of different sub-hypotheses was highly variable. Most noticeable, the conception that putative cancer stem cells are a rare subset of cells could not be confirmed by most studies (13.5% support). The empirical support varied also between types of cancer, animal models and cell isolation method used. For the first time, this study showed the applicability of the hierarchy-of-hypotheses approach for synthesizing and evaluating empirical evidence for a broad hypothesis in the field of bio-medical research.
| S-EPMC6910685 | biostudies-literature
Project description:The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana--SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD)--the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the "bird feeder effect") and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time.
| S-EPMC3130735 | biostudies-literature
Project description:Central questions to epigenome evolution include whether interspecies changes of histone modifications are independent of evolutionary changes of DNA, and if there is dependence whether they depend on any specific types of DNA sequence changes. Here, we present a likelihood approach for testing hypotheses on the co-evolution of genome and histone modifications. The gist of this approach is to convert evolutionary biology hypotheses into probabilistic forms, by explicitly expressing the joint probability of multispecies DNA sequences and histone modifications, which we refer to as a class of Joint Evolutionary Model for the Genome and the Epigenome (JEMGE). JEMGE can be summarized as a mixture model of four components representing four evolutionary hypotheses, namely dependence and independence of interspecies epigenomic variations to underlying sequence substitutions and to underlying sequence insertions and deletions (indels). We implemented a maximum likelihood method to fit the models to the data. Based on comparison of likelihoods, we inferred whether interspecies epigenomic variations depended on substitution or indels in local genomic sequences based on DNase hypersensitivity and spermatid H3K4me3 ChIP-seq data from human and rhesus macaque. Approximately 5.5% of homologous regions in the genomes exhibited H3K4me3 modification in either species, among which approximately 67% homologous regions exhibited local-sequence-dependent interspecies H3K4me3 variations. Substitutions accounted for less local-sequence-dependent H3K4me3 variations than indels. Among transposon-mediated indels, ERV1 insertions and L1 insertions were most strongly associated with H3K4me3 gains and losses, respectively. By initiating probabilistic formulation on the co-evolution of genomes and epigenomes, JEMGE helps to bring evolutionary biology principles to comparative epigenomic studies.
| S-EPMC6324829 | biostudies-literature
Project description:Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, 'simplicity is the ultimate sophistication'. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes. To fully appreciate streamlining, we must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche.
| S-EPMC4817614 | biostudies-literature
Project description:Environmental challenges to natural resources have been attributed to human behavior and traditional agricultural production techniques. Natural resource degradation in agriculture has always been a prime concern in agro ecological research and sustainability analysis. There are many techniques for assessing environmental performance; one of which, ecological footprint (EF), assesses human pressure on the environment and natural resources. The main purpose of this study was calculation of ecological indices including biocapacity (BC) and EF of rural areas of Fars province of Iran. The study was accomplished using survey and structured interviews consisting of three main questionnaires in two different steps. Different agricultural stakeholders, including farmers (for the first step) as well as the policymakers, extension managers and authorities (for the second step) were interviewed. Based on multi-stage stratified random sampling, 50 villages and 423 farmers were selected. Face validity and reliability of the questionnaires were assessed by a panel of specialists as well as conducting a pilot study, respectively. The paradigmatic perspectives of agricultural policy makers and managers (22 individuals) were also analyzed using another specific questionnaire by Analytical Hierarchy Process (AHP). Findings revealed that most of the studied villages faced a critical environmental condition due to the results of ecological indicator which was calculated in the study. According to the four main components of human ecology (POET model) including Population, Organization, Environment and Technology, village groups that differed in terms of sustainability level also showed significantly differences due to population, social participation, use of green technologies and attitude towards diverse environmental management paradigms. The causal model also revealed that population, green technology, social participation and attitude toward frontier economics, which were in accordance with the elements of human ecology model, were the main factors affecting the ecological index. Finally, AHP results determined the dominant economic perspectives of agricultural authorities. A paradigm shift toward the comprehensive paradigm of eco-development plus consideration of the results of the ecological indicator calculation as the base of agricultural planning at the local level were recommended.
| S-EPMC8051938 | biostudies-literature
Project description:There are many item response theory software packages designed for users. Here, the authors introduce an environment tailored to method development and simulation. Implementations of a selection of classic algorithms are available as well as some recently developed methods. Source code is developed in public repositories on GitHub; your collaboration is welcome.
| S-EPMC7495793 | biostudies-literature