scholarly journals Assessment of congruence between co-occurrence and functional networks: A new framework for revealing community assembly rules

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Gaëlle Legras ◽  
Nicolas Loiseau ◽  
Jean-Claude Gaertner ◽  
Jean-Christophe Poggiale ◽  
Dino Ienco ◽  
...  

AbstractDescribing how communities change over space and time is crucial to better understand and predict the functioning of ecosystems. We propose a new methodological framework, based on network theory and modularity concept, to determine which type of mechanisms (i.e. deterministic versus stochastic processes) has the strongest influence on structuring communities. This framework is based on the computation and comparison of two networks: the co-occurrence (based on species abundances) and the functional networks (based on the species traits values). In this way we can assess whether the species belonging to a given functional group also belong to the same co-occurrence group. We adapted the Dg index of Gauzens et al. (2015) to analyze congruence between both networks. This offers the opportunity to identify which assembly rule(s) play(s) the major role in structuring the community. We illustrate our framework with two datasets corresponding to different faunal groups and ecosystems, and characterized by different scales (spatial and temporal scales). By considering both species abundance and multiple functional traits, our framework improves significantly the ability to discriminate the main assembly rules structuring the communities. This point is critical not only to understand community structuring but also its response to global changes and other disturbances.

2015 ◽  
Author(s):  
Leonardo A Saravia

Species-area relationships (SAR) and species abundance distributions (SAD) are among the most studied patterns in ecology, due to their application to both theoretical and conservation issues. One problem with these general patterns is that different theories can generate the same predictions, and for this reason they cannot be used to detect different mechanisms of community assembly. A solution is to search for more sensitive patterns, for example by extending the SAR to the whole species abundance distribution. A generalized dimension ($D_q$) approach has been proposed to study the scaling of SAD, but to date there has been no evaluation of the ability of this pattern to detect different mechanisms. An equivalent way to express SAD is the rank abundance distribution (RAD). Here I introduce a new way to study SAD scaling using a spatial version of RAD: the species-rank surface (SRS), which can be analyzed using $D_q$. Thus there is an old $D_q$ based on SAR ($D_q^{SAD}$), and a new one based on SRS ($D_q^{SRS}$). I perform spatial simulations to examine the relationship of $D_q$ with SAD, spatial patterns and number of species. Finally I compare the power of both $D_q$, SAD, SAR exponent, and the fractal information dimension to detect different community patterns using a continuum of hierarchical and neutral spatially explicit models. The SAD, $D_q^{SAD}$ and $D_q^{SRS}$ all had good performance in detecting models with contrasting mechanisms. $D_q^{SRS}$, however, had a better fit to data and allowed comparisons between hierarchical communities where the other methods failed. The SAR exponent and information dimension had low power and should not be used. SRS and $D_q^{SRS}$ could be interesting methods to study community or macroecological patterns.


2002 ◽  
Vol 357 (1421) ◽  
pp. 667-681 ◽  
Author(s):  
Ricard V. Solé ◽  
David Alonso ◽  
Alan McKane

Why are some ecosystems so rich, yet contain so many rare species? High species diversity, together with rarity, is a general trend in neotropical forests and coral reefs. However, the origin of such diversity and the consequences of food web complexity in both species abundances and temporal fluctuations are not well understood. Several regularities are observed in complex, multispecies ecosystems that suggest that these ecologies might be organized close to points of instability. We explore, in greater depth, a recent stochastic model of population dynamics that is shown to reproduce: (i) the scaling law linking species number and connectivity; (ii) the observed distributions of species abundance reported from field studies (showing long tails and thus a predominance of rare species); (iii) the complex fluctuations displayed by natural communities (including chaotic dynamics); and (iv) the species–area relations displayed by rainforest plots. It is conjectured that the conflict between the natural tendency towards higher diversity due to immigration, and the ecosystem level constraints derived from an increasing number of links, leaves the system poised at a critical boundary separating stable from unstable communities, where large fluctuations are expected to occur. We suggest that the patterns displayed by species–rich communities, including rarity, would result from such a spontaneous tendency towards instability.


2020 ◽  
Vol 12 (2) ◽  
pp. 309 ◽  
Author(s):  
Jack H. Hastings ◽  
Scott V. Ollinger ◽  
Andrew P. Ouimette ◽  
Rebecca Sanders-DeMott ◽  
Michael W. Palace ◽  
...  

The ability to automatically delineate individual tree crowns using remote sensing data opens the possibility to collect detailed tree information over large geographic regions. While individual tree crown delineation (ITCD) methods have proven successful in conifer-dominated forests using Light Detection and Ranging (LiDAR) data, it remains unclear how well these methods can be applied in deciduous broadleaf-dominated forests. We applied five automated LiDAR-based ITCD methods across fifteen plots ranging from conifer- to broadleaf-dominated forest stands at Harvard Forest in Petersham, MA, USA, and assessed accuracy against manual delineation of crowns from unmanned aerial vehicle (UAV) imagery. We then identified tree- and plot-level factors influencing the success of automated delineation techniques. There was relatively little difference in accuracy between automated crown delineation methods (51–59% aggregated plot accuracy) and, despite parameter tuning, none of the methods produced high accuracy across all plots (27—90% range in plot-level accuracy). The accuracy of all methods was significantly higher with increased plot conifer fraction, and individual conifer trees were identified with higher accuracy (mean 64%) than broadleaf trees (42%) across methods. Further, while tree-level factors (e.g., diameter at breast height, height and crown area) strongly influenced the success of crown delineations, the influence of plot-level factors varied. The most important plot-level factor was species evenness, a metric of relative species abundance that is related to both conifer fraction and the degree to which trees can fill canopy space. As species evenness decreased (e.g., high conifer fraction and less efficient filling of canopy space), the probability of successful delineation increased. Overall, our work suggests that the tested LiDAR-based ITCD methods perform equally well in a mixed temperate forest, but that delineation success is driven by forest characteristics like functional group, tree size, diversity, and crown architecture. While LiDAR-based ITCD methods are well suited for stands with distinct canopy structure, we suggest that future work explore the integration of phenology and spectral characteristics with existing LiDAR as an approach to improve crown delineation in broadleaf-dominated stands.


2010 ◽  
Vol 16 ◽  
pp. 117-141 ◽  
Author(s):  
S. Kathleen Lyons ◽  
Felisa A. Smith

Macroecology is a rapidly growing sub-discipline within ecology that is concerned with characterizing statistical patterns of species' abundance, distribution and diversity at spatial and temporal scales typically ignored by traditional ecology. Both macroecology and paleoecology are concerned with answering similar questions (e.g., understanding the factors that influence geographic ranges, or the way that species assemble into communities). As such, macroecological methods easily lend themselves to many paleoecological questions. Moreover, it is possible to estimate the variables of interest to macroecologists (e.g., body size, geographic range size, abundance, diversity) using fossil data. Here we describe the measurement and estimation of the variables used in macroecological studies and potential biases introduced by using fossil data. Next we describe the methods used to analyze macroecological patterns and briefly discuss the current understanding of these patterns. This chapter is by no means an exhaustive review of macroecology and its methods. Instead, it is an introduction to macroecology that we hope will spur innovation in the application of macroecology to the study of the fossil record.


Ecology ◽  
2012 ◽  
Author(s):  
Herman A. Verhoef

At the beginning of the 20th century there was much debate about the “nature” of communities. The driving question was whether the community was a self-organized system of co-occurring species or simply a haphazard collection of populations with minimal functional integration. At that time, two extreme views dominated the discussion: one view considered a community as a superorganism, the member species of which were tightly bound together by interactions that contributed to repeatable patterns of species abundance in space and time. This concept led to the assumption that communities are fundamental entities, to be classified as the Linnaean taxonomy of species. Frederick E. Clements was one of the leading proponents of this approach, and his view became known as the organismic concept of communities. This assumes a common evolutionary history for the integrated species. The opposite view was the individualistic continuum concept, advocated by H. A. Gleason. His focus was on the traits of individual species that allow each to live within specific habitats or geographical ranges. In this view a community is an assemblage of populations of different species whose traits allow persisting in a prescribed area. The spatial boundaries are not sharp, and the species composition can change considerably. Consequently, it was discussed whether ecological communities were sufficiently coherent entities to be considered appropriate study objects. Later, consensus was reached: that properties of communities are of central interest in ecology, regardless of their integrity and coherence. From the 1950s and 1960s onward, the discussion was dominated by the deterministic outcome of local interactions between species and their environments and the building of this into models of communities. This approach, indicated as “traditional community ecology,” led to a morass of theoretical models, without being able to provide general principles about many-species communities. Early-21st-century approaches to bringing general patterns into community ecology concern (1) the metacommunity approach, (2) the functional trait approach, (3) evolutionary community ecology, and (4) the four fundamental processes. The metacommunity approach implicitly recognizes and studies the important role of spatiotemporal dynamics. In the functional trait approach, four themes are focused upon: traits, environmental gradients, the interaction milieu, and performance currencies. This functional, trait-focused approach should have a better prospect of understanding the effects of global changes. Evolutionary community ecology is an approach in which the combination of community ecology and evolutionary biology will lead to a better understanding of the complexity of communities and populations. The four fundamental processes are selection, drift, speciation, and dispersal. This approach concerns an organizational scheme for community ecology, based on these four processes to describe all existing specific models and frameworks, in order to make general statements about process–pattern connections.


2016 ◽  
Author(s):  
Bjarte Hannisdal ◽  
Kristian A. Haaga ◽  
Trond Reitan ◽  
David Diego ◽  
Lee Hsiang Liow

Common species shape the world around us, and changes in their commonness signify large-scale shifts in ecosystem structure and function. Dominant taxa drive productivity and biogeochemical cycling, in direct interaction with abiotic components of the Earth system. However, our understanding of the dynamic response of ecosystems to global environmental changes in the past is limited by our ability to robustly estimate fossil taxonomic richness, and by our neglect of the importance of common species. To rectify this, we use observations of the most common and widespread species to track global changes in their distribution in the deep geological past. Our simple approach is robust to factors that bias richness estimators, including widely used sampling-standardization methods, which we show are highly sensitive to variability in the species-abundance distribution. Causal analyses of common species frequency in the deep-sea sedimentary record detect a lagged response in the ecological prominence of planktonic foraminifera to oceanographic changes captured by deep-ocean temperature records over the last 65 million years, encompassing one of Earth's major climate transitions. Our results demonstrate that common species can act as tracers of a past global ecosystem and its response to physical changes in Earth's dynamic history.


2015 ◽  
Author(s):  
Daijiang Li ◽  
Anthoy R Ives ◽  
Donald M Waller

Phylogeny-based and functional trait-based analyses are two principle ways to study community assembly and underlying ecological processes. In principle, knowing all information about species traits would make phylogenetic information redundant, at least that component of phylogenetic signal in the distribution of species among communities that is caused by phylogenetically related species sharing similar traits. In reality, phylogenies may contain more information than a set of singular, discretely measured traits because we cannot measure all species traits and may misjudge which are most important. The extent to which functional trait information makes phylogenetic information redundant, however, has not been explicitly studied with empirical data in community ecology. Here, we use phylogenetic linear mixed models to analyze community assembly of 55 understory plant species in 30 forest sites in central Wisconsin. These communities show strong phylogenetic attraction, yet variation among sites in 20 environmental variables could not account for this pattern. Most of the 15 functional traits we measured had strong phylogenetic signal, but only three varied strongly among sites in ways that affected species' abundances. These three traits explained only 19% of variation in phylogenetic patterns of species co-occurrence. Thus, phylogenies appear to provide considerably more information about community assembly than the functional traits measured in this study, demonstrating the value of phylogeny in studying of community assembly processes even with abundant functional traits.


2021 ◽  
Author(s):  
Joséphine Couet ◽  
Emma-Liina Marjakangas ◽  
Andrea Santangeli ◽  
John Atle Kålås ◽  
Åke Lindström ◽  
...  

Abstract Climate change is pushing species ranges towards poles and mountain tops. Although many studies have documented local altitudinal shifts, knowledge of general patterns at a large spatial scale, such as a whole mountain range, is very limited. From a conservation perspective, studying altitudinal shifts is particularly important as mountain regions often represent biodiversity hotspots and are among the most vulnerable ecosystems. Here, we examine whether altitudinal shifts have occurred among birds in the Scandinavian mountains over 13 years and assess whether such shifts are related to species’ traits. Using abundance data, we show a clear pattern of uphill shifts in the mean altitudes of the bird species’ abundances across the Scandinavian mountains, with an average speed of 0.9 m per year. Out of 77 species, 54 shifted their ranges uphill. In general, the range shift was faster when the altitudinal range within the area was wider. Importantly, the altitudinal shift was strongly related to species’ longevity: short-lived species showed more pronounced altitudinal uphill shifts than long-lived species. Our results show that the altitudinal range shifts are not only driven by a small number of individuals at the range boundaries, but the overall bird abundances are on the move. This highlights the wide-ranging impact of climate change and the potential vulnerability of species with slow life-histories, as they appear unable to timely respond to rapidly changing climatic conditions.


Author(s):  
Pedro Giovâni da Silva

β-diversity is a key measure to understand biodiversity patterns across spatial and temporal scales. In this study, two published datasets on dung beetle (Coleoptera: Scarabaeinae) from Brazilian Pampa are re-analyzed aiming to investigate the role of β-diversity process-related components based on composition- and abundance-based approaches for both spatial (grassland-forest ecotone) and temporal (samplings along a year) scales. Dung beetles were sampled in a grassland-forest ecotone in October 2006 and in a grassland area monthly during an entire year (December 2006 to November 2007), using baited pitfall traps. β-diversity was decomposed into turnover and nestedness-resultant components based on Jaccard dissimilarity coefficient, and also into balanced variation in abundance and abundance gradients based on Bray-Curtis dissimilarity coefficient. Both environmental (spatial scale) and climatic (temporal scale) differences affected dung beetles similarly in terms of species replacement and nestedness patterns, and similarly in terms of variation in abundance and abundance gradients. For both spatial and temporal approach, the species turnover and the variation in species abundances were higher, while nestedness patterns and abundance gradients were of minor relative importance.


Ecosphere ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Murilo Dantas de Miranda ◽  
Luís Borda‐de‐Água ◽  
Henrique Miguel Pereira ◽  
Thomas Merckx

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