Trends in ecology: shifts in ecological research themes over the past four decades

McCallen, Emily B.; Knott, Jonathan; Nunez‐Mir, Gabriela C.; Taylor, Benjamin; Jo, Insu; Fei, Songlin

doi:10.1002/fee.1993

Cited by 102 publications

(139 citation statements)

References 33 publications

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“…We inferred trends in topic prevalence over time by averaging topic prevalence change between two consecutive year groups. Topics with positive and negative averages in prevalence over time were considered hot topics (growing popularity) and cold topics (decreasing popularity), respectively (following Griffiths & Steyvers, 2004;McCallen et al, 2019).…”

Section: Topic Popularitymentioning

confidence: 99%

“…Topics with positive and negative averages in prevalence over time were considered hot topics (growing popularity) and cold topics (decreasing popularity), respectively (followingGriffiths & Steyvers, 2004;McCallen et al, 2019). The exception to this was for the 1970-1979 decade, which was treated as a single group due to the relatively small number of papers published in this period and thereby avoids a disproportional influence of a few articles at the beginning of our sampling period.…”

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confidence: 99%

“…Topic modelling is commonly used in political, economic and literature sciences. However, lately this approach has shown considerable promise in ecology and conservation (Chandelier, Steuckardt, Mathevet, Diwersy, & Gimenez, 2018;Greenville, Dickman, & Wardle, 2017;McCallen et al, 2019;Westgate, Barton, Pierson, & Lindenmayer, 2015), and in the aquatic sciences (Syed, Borit, & Spruit, 2018). As publications continue to…”

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confidence: 99%

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Trait‐based ecology of fishes: A quantitative assessment of literature trends and knowledge gaps using topic modelling

et al. 2019

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Species traits are a new data currency to enhance our understanding of ecological patterns and processes. Trait‐based studies of fishes are numerous in comparison with other animal groups, reflecting the diversity of fish forms and functions they provide to aquatic ecosystems. We conduct a retrospective examination of literature to identify knowledge gaps and provide guidance for future research in trait‐based fish ecology. We apply an automated text mining and topic modelling to track the evolution of research topics within peer‐reviewed articles of functional traits in marine and freshwater fishes published over the past half century, explore the inter‐connections among those topics and identify emerging avenues for investigation. By mapping the topic landscape of the literature, 16 latent topics emerged that vary in their prevalence. Our results show a decline in the frequency of studies using reproductive traits to model and explore the way fish allocate energy for reproduction, and increase in studies reporting functional diversity metrics and utilizing the concept of multivariate functional space. Research focused on contributions of fish traits to ecosystem functioning also has increased in frequency. We revealed large gaps in information between growing and decreasing topics and that these gaps were derived from different types of traits being considered. We suggest that scientists break‐free from the traditions of their research field by targeting investigations that: (a) apply functional diversity metrics to a broader assortment of traits, (b) focus on traits influencing energy allocation to growth/reproduction and (c) integrate trophic‐web and behavioural studies with other topics.

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Section: Topic Popularitymentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Trait‐based ecology of fishes: A quantitative assessment of literature trends and knowledge gaps using topic modelling

et al. 2019

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“…The direction of the arrows indicates "usage." More granular approaches, such as topic models and automated content analysis (Blei, Ng, & Jordan, 2003;McCallen et al,2019), analyze word co-occurrence patterns within articles and classify them into similar concepts to explore patterns of interdisciplinarity. In this framework, "SD1" would be the most diverse and conceptually heterogeneous subdiscipline (as indicated by the blue arrows connecting it to three concepts), and "SD3" would be the least diverse and most conceptually homogeneous subdiscipline (as indicated by the blue arrow connecting it to only one concept), while "Concept 3" would be the most interdisciplinary concept (as indicated by the orange arrows connecting it to three subdisciplines), and "Concept 4" would be the least interdisciplinary concept (as indicated by the orange arrow connecting it to only one subdiscipline) al., 2017).…”

Section: Me Thodsmentioning

confidence: 99%

Evolution of interdisciplinarity in biodiversity science

Craven

Winter

Hotzel³

et al. 2019

Ecology and Evolution

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The study of biodiversity has grown exponentially in the last thirty years in response to demands for greater understanding of the function and importance of Earth's biodiversity and finding solutions to conserve it. Here, we test the hypothesis that biodiversity science has become more interdisciplinary over time. To do so, we analyze 97,945 peer‐reviewed articles over a twenty‐two‐year time period (1990–2012) with a continuous time dynamic model, which classifies articles into concepts (i.e., topics and ideas) based on word co‐occurrences. Using the model output, we then quantify different aspects of interdisciplinarity: concept diversity, that is, the diversity of topics and ideas across subdisciplines in biodiversity science, subdiscipline diversity, that is, the diversity of subdisciplines across concepts, and network structure, which captures interactions between concepts and subdisciplines. We found that, on average, concept and subdiscipline diversity in biodiversity science were either stable or declining, patterns which were driven by the persistence of rare concepts and subdisciplines and a decline in the diversity of common concepts and subdisciplines, respectively. Moreover, our results provide evidence that conceptual homogenization, that is, decreases in temporal β concept diversity, underlies the observed trends in interdisciplinarity. Together, our results reveal that biodiversity science is undergoing a dynamic phase as a scientific discipline that is consolidating around a core set of concepts. Our results suggest that progress toward addressing the biodiversity crisis via greater interdisciplinarity during the study period may have been slowed by extrinsic factors, such as the failure to invest in research spanning across concepts and disciplines. However, recent initiatives such as the Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services (IPBES) may attract broader support for biodiversity‐related issues and hence interdisciplinary approaches to address scientific, political, and societal challenges in the coming years.

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“…In particular, the extent to which an environmental shift affects the system's behaviour. 19 Introduction 22 Despite the primacy of evolution in biology, there remains the critical gap in our understanding of how 23 environment influences evolution [1]. This is especially relevant for environmental changes from the 24 scale of small groups to global climatic events.…”

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confidence: 99%

Shifts in evolutionary balance of microbial phenotypes under environmental changes

Kleshnina

McKerral

González-Tokman

et al. 2020

Preprint

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5Environmental conditions shape entire communities by driving microbial interactions. These 6 interactions then find their reflection in the evolutionary outcome of microbial competition. In static, 7 homogeneous environments a robust, or evolutionary stable, outcome in microbial communities is 8 reachable, if it exists. However, introducing heterogeneity and time-dependence in microbial ecology 9 leads to stochastic evolutionary outcomes determined by specific environmental changes. We utilise 10 evolutionary game theory to provide insight into phenotypic competition in dynamic environments. 11 We capture these effects in a perturbed evolutionary game describing microbial interactions at a 12 phenotypic level. We show that under regular periodic environmental fluctuations a stable state that 13 preserves dominant phenotypes is reached. However, rapid environmental shifts, especially in a 14 cyclic interactions, can lead to critical shifts in the evolutionary balance among phenotypes. Our 15 analysis suggests that an understanding of the robustness of the systems current state is necessary to 16 understand when system will shift to the new equilibrium. This can be done by understanding the 17 1 systems overall margin of safety, that is, what level of perturbations it can take before its equilibrium 18 changes. In particular, the extent to which an environmental shift affects the system's behaviour. 19 Introduction 22 Despite the primacy of evolution in biology, there remains the critical gap in our understanding of how 23 environment influences evolution [1]. This is especially relevant for environmental changes from the 24 scale of small groups to global climatic events. However, the timescales for genetic adaptation are often 25 slower than environmental changes, meaning that the important response is in the phenotype. 26Bacteria are ideal model systems for studying phenotypic response due to their rapid reproduction, 27 comparatively simple biology, and suitability for laboratory study. With most bacterial sensory systems 28 limited to molecular uptake, it is impossible for them to anticipate environmental changes. As the most 29 abundant life on earth, bacteria regulate the biosphere while being intimately connected to it. A single 30 bacterial species, unlike animals, may rapidly change its role from abundant to rare, and from dominant-31 aggressive to rare-passive or some mix of the two depending on local habitat [2,3]. This may lead to trait 32 variation in originally genetically identical organisms [4]. Microbial research often focuses on coopera-33 tion or competition among species, extending experimental findings to evolutionary models [5][6][7][8]. The 34 intra-specific interactions are often overlooked. However, it is within species phenotypic variation that 35 shapes genetic drift, which subsequently determines the genome evolution behind inter-specific interac-36 tions. 37For identical genotypes in a static environments reaction to stimuli can be distinct [9]. Stochasticity in 38 gene expre...

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Trends in ecology: shifts in ecological research themes over the past four decades

Cited by 102 publications

References 33 publications

Trait‐based ecology of fishes: A quantitative assessment of literature trends and knowledge gaps using topic modelling

Trait‐based ecology of fishes: A quantitative assessment of literature trends and knowledge gaps using topic modelling

Evolution of interdisciplinarity in biodiversity science

Shifts in evolutionary balance of microbial phenotypes under environmental changes

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