scholarly journals Emergent phases of ecological diversity and dynamics mapped in microcosms

2021 ◽  
Author(s):  
Jiliang Hu ◽  
Daniel R. Amor ◽  
Matthieu Barbier ◽  
Guy Bunin ◽  
Jeff Gore
Keyword(s):  
Species Interactions ◽  
Stable Equilibrium ◽  
Species Abundance ◽  
Ecological Communities ◽  
Ecological Diversity ◽  
Unified Framework ◽  
Complex Systems Theory ◽  
Microbial Ecosystems ◽  
Wide Range ◽  
Emergent Behaviors

Natural ecological communities display striking features, such as high biodiversity and a wide range of dynamics, that have been difficult to explain in a unified framework. Using experimental bacterial microcosms, we perform the first direct test of recent complex systems theory predicting that simple aggregate parameters dictate emergent behaviors of the community. As either the number of species or the strength of species interactions is increased, we show that microbial ecosystems transition between distinct qualitative dynamical phases in the predicted order, from a stable equilibrium where all species coexist, to partial coexistence, to emergence of persistent fluctuations in species abundance. Under the same conditions, high biodiversity and fluctuations allow and require each other. Our results demonstrate predictable emergent diversity and dynamics in ecological communities.

scholarly journals Idea Paper: improving forecasts of community composition with lightweight biodiversity monitoring across ecological and anthropogenic disturbance gradients

2021 ◽  
Author(s):  
Jamie M. Kass ◽  
Nao Takashina ◽  
Nicholas Friedman ◽  
Buntarou Kusumoto ◽  
Mary E. Blair
Keyword(s):  
Community Composition ◽  
Species Interactions ◽  
Anthropogenic Disturbance ◽  
Ecological Communities ◽  
Geographic Patterns ◽  
Wide Range ◽  
Community Data ◽  
Passive Sensors ◽  
Different Dimensions ◽  
Management And Conservation

Accurate and up-to-date biodiversity forecasts enable robust planning for environmental management and conservation of landscapes under a wide range of uses. Future predictions of the species composition of ecological communities complement more frequently reported species richness estimates to better characterize the different dimensions of biodiversity. The models that make community composition forecasts are calibrated with data on species’ geographic patterns for the present, which may not be good proxies for future patterns. The future establishment of novel communities represents data on species interactions unaccounted for by these models. However, detecting them in a systematic way presents challenges due to the lack of monitoring data for landscapes with high environmental turnover, where such communities are likely to establish. Here, we propose lightweight monitoring over both ecological and anthropogenic disturbance gradients using passive sensors (i.e., those that operate continuously without much human input) to detect novel communities with the aim of updating models that make community composition forecasts. Monitoring over these two gradients should maximize detection of novel communities and improve understanding of relationships between community composition and environmental change. Further, barriers regarding cost and effort are reduced by using relatively few sensors requiring minimal upkeep. Ongoing updates to community composition forecasts based on novel community data and better understanding of the associated uncertainty should improve future decision-making for both resource management and conservation efforts.

scholarly journals A process-based metacommunity framework linking local and regional scale community ecology

2019 ◽  
Author(s):  
Patrick L. Thompson ◽  
Laura Melissa Guzman ◽  
Luc De Meester ◽  
Zsófia Horváth ◽  
Robert Ptacnik ◽  
...  
Keyword(s):  
Simulation Model ◽  
Community Ecology ◽  
Species Interactions ◽  
Community Dynamics ◽  
Regional Scale ◽  
Ecological Communities ◽  
Data Accessibility ◽  
Species Sorting ◽  
Wide Range ◽  
Underlying Processes

AbstractThe metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: 1) density-independent responses to abiotic conditions, 2) density-dependent biotic interactions, and 3) dispersal. Stochasticity is incorporated in the demographic realization of each of these processes. We formalize this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning, and stability within metacommunities.Statement of authorshipThis project was conceived at the sTURN working group, of which all authors are members. PLT developed the framework and model with input from all authors. PLT wrote the model code. PLT and LMG performed the simulations. PLT produced the figures and wrote the first draft with input from LMG and JMC. All authors provided feedback and edits on several versions of the manuscript.Data accessibilityAll code for running the simulation model and producing the figures is archived on Zenodo - https://doi.org/10.5281/zenodo.3833035.

scholarly journals Fuzzy Quantification of Common and Rare Species in Ecological Communities (FuzzyQ)

2020 ◽  
Author(s):  
Juan A. Balbuena ◽  
Clara Montlleó ◽  
Cristina Llopis-Belenguer ◽  
Isabel Blasco-Costa ◽  
Volodimir L. Sarabeev ◽  
...  
Keyword(s):  
Rare Species ◽  
Clustering Algorithm ◽  
Species Abundance ◽  
R Package ◽  
Ecological Communities ◽  
Wide Range ◽  
Species Abundance Distributions ◽  
The Common ◽  
Spatio Temporal ◽  
The Impact

Abstract1. Most species in ecological communities are rare whereas only a few are common. This distributional paradox has intrigued ecologists for decades but the interpretation of species abundance distributions remains elusive.2. We present Fuzzy Quantification of Common and Rare Species in Ecological Communities (FuzzyQ) as an R package. FuzzyQ shifts the focus from the prevailing species-categorization approach to develop a quantitative framework that seeks to place each species along a rare-commonness gradient. Given a community surveyed over a number of sites, quadrats, or any other convenient sampling unit, FuzzyQ uses a fuzzy clustering algorithm that estimates a probability for each species to be common or rare based on abundance-occupancy information. Such as probability can be interpreted as a commonness index ranging from 0 to 1. FuzzyQ also provides community-level metrics about the coherence of the allocation of species into the common and rare clusters that are informative of the nature of the community under study.3. The functionality of FuzzyQ is shown with two real datasets. We demonstrate how FuzzyQ can effectively be used to monitor and model spatio-temporal changes in species commonness, and assess the impact of species introductions on ecological communities. We also show that the approach works satisfactorily with a wide range of communities varying in species richness, dispersion and abundance currencies.4. FuzzyQ produces ecological indicators easy to measure and interpret that can give both clear, actionable insights into the nature of ecological communities and provides a powerful way to monitor environmental change on ecosystems. Comparison among communities is greatly facilitated by the fact that the method is relatively independent of the number of sites or sampling units considered. Thus, we consider FuzzyQ as a potentially valuable analytical tool in community ecology and conservation biology.

scholarly journals Higher order interactions and species coexistence

2020 ◽  
Author(s):  
Pragya Singh ◽  
Gaurav Baruah
Keyword(s):  
Intraspecific Competition ◽  
Species Interactions ◽  
Species Coexistence ◽  
General Rule ◽  
Higher Order ◽  
Volterra Model ◽  
Ecological Communities ◽  
Wide Range ◽  
Analytical Result ◽  
Underlying Mechanisms

AbstractHigher order interactions (HOIs) have been suggested to stabilize diverse ecological communities. However, their role in maintaining species coexistence from the perspective of modern coexistence theory is not known. Here, using generalized Lotka-Volterra model, we derive a general rule for species coexistence modulated by HOIs. We show that where pairwise species interactions fail to promote species coexistence in regions of extreme fitness differences, negative HOIs that intensify pairwise competition, however, can promote coexistence provided that HOIs strengthen intraspecific competition more than interspecific competition. In contrast, positive HOIs that alleviate pairwise competition can stabilize coexistence across a wide range of fitness differences, irrespective of differences in strength of inter- and intraspecific competition. In addition, we extend our three-species analytical result to multispecies communities and show, using simulations, that multispecies coexistence is possible provided that strength of negative intraspecific HOIs is higher than interspecific HOIs. Our work sheds light on the underlying mechanisms through which HOIs can maintain species diversity.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals Cycle and flow trusses in directed networks

2016 ◽  
Vol 3 (11) ◽  
pp. 160270 ◽  
Author(s):  
Taro Takaguchi ◽  
Yuichi Yoshida
Keyword(s):  
Truss Structures ◽  
Directed Network ◽  
Unified Framework ◽  
Directed Networks ◽  
Research Fields ◽  
Wide Range ◽  
Definition Of ◽  
Information Finding ◽  
Empirical Networks ◽  
Module Structures

When we represent real-world systems as networks, the directions of links often convey valuable information. Finding module structures that respect link directions is one of the most important tasks for analysing directed networks. Although many notions of a directed module have been proposed, no consensus has been reached. This lack of consensus results partly because there might exist distinct types of modules in a single directed network, whereas most previous studies focused on an independent criterion for modules. To address this issue, we propose a generic notion of the so-called truss structures in directed networks. Our definition of truss is able to extract two distinct types of trusses, named the cycle truss and the flow truss, from a unified framework. By applying the method for finding trusses to empirical networks obtained from a wide range of research fields, we find that most real networks contain both cycle and flow trusses. In addition, the abundance of (and the overlap between) the two types of trusses may be useful to characterize module structures in a wide variety of empirical networks. Our findings shed light on the importance of simultaneously considering different types of modules in directed networks.

scholarly journals A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees

2017 ◽  
Vol 284 (1846) ◽  
pp. 20162395 ◽  
Author(s):  
Kohei Koyama ◽  
Ken Yamamoto ◽  
Masayuki Ushio
Keyword(s):  
Lognormal Distribution ◽  
Species Abundance ◽  
Self Similarity ◽  
Lognormal Distributions ◽  
Multiplicative Effect ◽  
Wide Range ◽  
Error Distributions ◽  
Species Abundance Distributions ◽  
Self Similar ◽  
Ulmus Davidiana

Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of multicellular organismal forms. We tested the hypotheses that the distribution of the lengths of terminal stems of Japanese elm trees ( Ulmus davidiana ), the end products of a self-similar branching process, approaches a lognormal distribution. We measured the length of the stem segments of three elm branches and obtained the following results: (i) each occurrence of branching caused variations or errors in the lengths of the child stems relative to their parent stems; (ii) the branches showed statistical self-similarity; the observed error distributions were similar at all scales within each branch and (iii) the multiplicative effect of these errors generated variations of the lengths of terminal twigs that were well approximated by a lognormal distribution, although some statistically significant deviations from strict lognormality were observed for one branch. Our results provide the first empirical evidence that statistical self-similarity of an organismal form generates a lognormal distribution of organ sizes.

Cooperation between Species

2017 ◽  
Author(s):  
Raymond Pierotti ◽  
Brandy R. Fogg
Keyword(s):  
Cooperative Behavior ◽  
Natural World ◽  
Western Science ◽  
Ecological Communities ◽  
Cooperative Hunting ◽  
Wide Range

This chapter reviews the study of cooperative behavior between species, with emphasis on examples of cooperative hunting found in a wide range of species. Seen in this context, the idea of cooperative hunting between humans and wolves that evolved into present relationships with dogs does not seem unusual or surprising. The chapter then critiques the proposal that competition between species is more important than cooperation in structuring ecological communities, discussing how this notion leads to a suite of ideas philosophically separating humans from the rest of the natural world. In many ways Western science is unintentionally complicit in such thinking. The chapter concludes by discussing complex cooperation, including long-term relationships between members of different species.

scholarly journals SEAMUS (v1.0): a Δ<sup>14</sup>C-enabled, single-specimen sediment accumulation simulator

2019 ◽  
Author(s):  
Bryan C. Lougheed
Keyword(s):  
Sediment Core ◽  
Accumulation Rate ◽  
Sediment Accumulation ◽  
Species Abundance ◽  
Depth Interval ◽  
Single Specimen ◽  
14C Dating ◽  
Deep Sea Sediment ◽  
Wide Range ◽  
History Of

Abstract. The systematic bioturbation of single particles (such as foraminifera) within deep-sea sediment archives leads to the apparent smoothing of any temporal signal as record by the downcore, discrete-depth mean signal. This smoothing is the result of the systematic mixing of particles from a wide range of depositional ages into the same discrete depth interval. Previous sediment models that simulate bioturbation have specifically produced an output in the form of a downcore, discrete-depth mean signal. Palaeoceanographers analysing the distribution of single foraminifera specimens from sediment core intervals would be assisted by a model that specifically evaluates the effect of bioturbation upon single specimen populations. Taking advantage of recent increases in computer memory, the single-specimen SEdiment AccuMUlation Simulator (SEAMUS) was created in Matlab, whereby large arrays of single specimens are simulated. This simulation allows researchers to analyse the post-bioturbation age heterogeneity of single specimens contained within discrete-depth sediment core intervals, and how this heterogeneity is influenced by changes in sediment accumulation rate (SAR), bioturbation depth (BD) and species abundance. The simulation also assigns a realistic 14C activity to each specimen, by considering the dynamic Δ14C history of the Earth and temporal changes in reservoir age. This approach allows for the quantification of possible significant artefacts arising when 14C dating multi-specimen samples with heterogeneous 14C activity. Users may also assign additional desired carrier signals to specimens (e.g., stable isotopes, trace elements, temperature, etc.) and consider a second species with an independent abundance. Finally, the model can simulate a virtual palaeoceanographer by randomly picking whole specimens (whereby the user can set the percentage of older, broken specimens) of a prescribed sample size from discrete depths, after which virtual laboratory 14C dating and 14C calibration is carried out within the model.

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