scholarly journals Food web reconstruction through phylogenetic transfer of low-rank network representation

2021 ◽  
Author(s):  
Tanya Strydom ◽  
Salomé Bouskila ◽  
Francis Banville ◽  
Cerres Barros ◽  
Dominique Caron ◽  
...  

Despite their importance in many ecological processes, collecting data and information on ecological interactions, and therefore species interaction networks, is an exceedingly challenging task. For this reason, large parts of the world have a deficit of data of which species interact, and what we can expect the network structure of these interactions to be. As data collection alone is unlikely to be sufficient at filling these global gaps, community ecologists must adopt predictive methods. In this contribution we develop such a method, relying on graph embedding (the extraction of explanatory latent variables from known graph structures) and transfer learning (the application of previous solution to novel problems with limited predictors overlap) in order to assemble a predicted list of trophic interactions between mammals of Canada. This interaction list is derived from extensive knowledge of the mammalian food web of Europe, despite the fact that there are fewer than 5% of common species between the two locations. We provide guidance on how this method can be adapted by substituting some approaches or predictors in order to make it more generally applicable to a broad family of ecological problems.

2018 ◽  
Vol 373 (1761) ◽  
pp. 20170435 ◽  
Author(s):  
Emma-Liina Marjakangas ◽  
Luísa Genes ◽  
Mathias M. Pires ◽  
Fernando A. S. Fernandez ◽  
Renato A. F. de Lima ◽  
...  

Trophic rewilding has been suggested as a restoration tool to restore ecological interactions and reverse defaunation and its cascading effects on ecosystem functioning. One of the ecological processes that has been jeopardized by defaunation is animal-mediated seed dispersal. Here, we propose an approach that combines joint species distribution models with occurrence data and species interaction records to quantify the potential to restore seed-dispersal interactions through rewilding and apply it to the Atlantic Forest, a global biodiversity hotspot. Using this approach, we identify areas that should benefit the most from trophic rewilding and candidate species that could contribute to cash the credit of seed-dispersal interactions in a given site. We found that sites within large fragments bearing a great diversity of trees may have about 20 times as many interactions to be cashed through rewilding as small fragments in regions where deforestation has been pervasive. We also ranked mammal and bird species according to their potential to restore seed-dispersal interactions if reintroduced while considering the biome as a whole and at finer scales. The suggested approach can aid future conservation efforts in rewilding projects in defaunated tropical rainforests. This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change’.


Author(s):  
Paula Schirrmacher ◽  
Christina C. Roggatz ◽  
David M. Benoit ◽  
Jörg D. Hardege

AbstractWith carbon dioxide (CO2) levels rising dramatically, climate change threatens marine environments. Due to increasing CO2 concentrations in the ocean, pH levels are expected to drop by 0.4 units by the end of the century. There is an urgent need to understand the impact of ocean acidification on chemical-ecological processes. To date, the extent and mechanisms by which the decreasing ocean pH influences chemical communication are unclear. Combining behaviour assays with computational chemistry, we explore the function of the predator related cue 2-phenylethylamine (PEA) for hermit crabs (Pagurus bernhardus) in current and end-of-the-century oceanic pH. Living in intertidal environments, hermit crabs face large pH fluctuations in their current habitat in addition to climate-change related ocean acidification. We demonstrate that the dietary predator cue PEA for mammals and sea lampreys is an attractant for hermit crabs, with the potency of the cue increasing with decreasing pH levels. In order to explain this increased potency, we assess changes to PEA’s conformational and charge-related properties as one potential mechanistic pathway. Using quantum chemical calculations validated by NMR spectroscopy, we characterise the different protonation states of PEA in water. We show how protonation of PEA could affect receptor-ligand binding, using a possible model receptor for PEA (human TAAR1). Investigating potential mechanisms of pH-dependent effects on olfactory perception of PEA and the respective behavioural response, our study advances the understanding of how ocean acidification interferes with the sense of smell and thereby might impact essential ecological interactions in marine ecosystems.


Geografie ◽  
1989 ◽  
Vol 94 (1) ◽  
pp. 19-30
Author(s):  
Galina Kruglová ◽  
Jan Vaněk

The paper treats of harmful influences of the industrial sprawl, of ecological processes and phenomena interfering with socio-economic functions of the North Bohemian landscape. Great attention has been paid to special ecological problems related to open-cast mining, brown-coal preparation, uranium-ore mining, development of power stations, chemistry, land other industrial branches. According to the degree of anthropogenic influences owing to complex multi-line land use and conforming with ecological aspects, three types of regions have defined in the North Bohemian region.


2009 ◽  
Vol 69 (3) ◽  
pp. 843-849 ◽  
Author(s):  
IA. Silva ◽  
MA. Batalha

Ecological communities are the result of not only present ecological processes, such as competition among species and environmental filtering, but also past and continuing evolutionary processes. Based on these assumptions, we may infer mechanisms of contemporary coexistence from the phylogenetic relationships of the species in a community. We studied the phylogenetic structure of plant communities in four cerrado sites, in southeastern Brazil. We calculated two raw phylogenetic distances among the species sampled. We estimated the phylogenetic structure by comparing the observed phylogenetic distances to the distribution of phylogenetic distances in null communities. We obtained null communities by randomizing the phylogenetic relationships of the regional pool of species. We found a phylogenetic overdispersion of the cerrado species. Phylogenetic overdispersion has several explanations, depending on the phylogenetic history of traits and contemporary ecological interactions. However, based on coexistence models between grasses and trees, density-dependent ecological forces, and the evolutionary history of the cerrado flora, we argue that the phylogenetic overdispersion of cerrado species is predominantly due to competitive interactions, herbivores and pathogen attacks, and ecological speciation. Future studies will need to include information on the phylogenetic history of plant traits.


2018 ◽  
Vol 193 ◽  
pp. 01033
Author(s):  
Kseniya Kovalenko ◽  
Nataliya Kovalenko

This article considers the main types of global environmental problems as crisis ecological situations that are relevant for the entire planet, the solution of which is possible only with the participation of all humanity. Global environmental problems closely related to other global world problems, they affect each other and the emergence of some leads to the emergence or aggravation of others. The paper is concerned that such a complex world problem as the demographic caused by the explosive growth of the world's population leads to a sharp increase in the burden on the environment due to an increase in people's needs for food, energy, housing, industrial goods, etc. Obviously, without solving the demographic problem, without stabilizing the population, it is impossible to restrain the development of crisis ecological processes on the planet. In turn, the ecological problems of desertification, deforestation, causing degradation and loss of agricultural land, lead to an aggravation of the world food problem. The ecological danger of such global problem as military is great. In this article, we have determined that environmental degradation leads to significant economic costs as a result of degradation of natural resources, pollution, deterioration of public health.


2019 ◽  
Author(s):  
Carine Emer ◽  
Pedro Jordano ◽  
Marco A. Pizo ◽  
Milton C. Ribeiro ◽  
Fernanda R. da Silva ◽  
...  

ABSTRACTSeed dispersal interactions involve key ecological processes in tropical forests that help to maintain ecosystem functioning. Yet this functionality may be threatened by increasing habitat loss, defaunation and fragmentation. However, generalist species, and their interactions, can benefit from the habitat change caused by human disturbance while more specialized interactions mostly disappear. Therefore changes in the structure of the local, within fragment, networks can be expected. Here we investigated how the structure of seed-dispersal networks changes along a gradient of increasing habitat fragmentation. We analysed 16 bird seed-dispersal assemblages from forest fragments of a biodiversity-rich ecosystem. We found significant species-, interaction- and network-area relationships, yet the later was determined by the number of species remaining in each community. The number of frugivorous bird and plant species, their interactions, and the number of links per species decreases as area is lost in the fragmented landscape. In contrast, network nestedness has a negative relationship with fragment area, suggesting an increasing generalization of the network structure in the gradient of fragmentation. Network specialization was not significantly affected by area, indicating that some network properties may be invariant to disturbance. Still, the local extinction of partner species, paralleled by a loss of interactions and specialist-specialist bird-plant seed dispersal associations suggests the functional homogenization of the system as area is lost. Our study provides empirical evidence for network-area relationships driven by the presence/absence of remnant species and the interactions they perform.RESUMOInterações de dispersão de sementes formam um processo ecológico chave em florestas tropicais onde colaboram na manutenção do funcionamento do ecossistema. Porém, esta funcionalidade pode estar ameaçada pelo aumento na perda e fragmentação do habitat. Enquanto espécies generalistas e suas interações podem se beneficiar da mudança de habitat causada por distúrbios antrópicos, interações envolvendo espécies mais especialistas são, na maioria, eliminadas. Desta forma, mudanças nas redes locais, dentro de fragmentos florestais, são esperadas. Neste trabalho nós investigamos como a estrutura de redes de dispersão de sementes mudam em um gradiente de fragmentação do habitat. Nós analisamos 16 comunidades de dispersão de sementes espacialmente explícitas e distribuídas em fragmentos florestais de um ecossistema rico em biodiversidade. Nós encontramos relações significativas entre a área do fragmento e espécies, interações e estrutura das redes, sendo que o último foi determinado pelo número de espécies remanescentes em cada comunidade. O número de espécies de aves frugívoras e plantas e as interações entre eles, bem como o número de links por espécie diminuíram significativamente conforme a área dos fragmentos é perdida. Por outro lado, o aninhamento da rede mostrou uma relação negativa com a área do fragmento, sugerindo um aumento da generalização da estrutura das redes com a fragmentação do habitat. No entanto, o grau de especialização das redes não foi afetado pela área, indicando que algumas propriedades de rede podem ser resistentes à perturbação. Sendo assim, a extinção local de espécies parceiras, conjuntamente com a perda das interações e associações planta-dispersor mais especializadas, sugere uma homogeneização do sistema conforme a área do fragmento é perdida. Nosso estudo fornece evidências empíricas para as relações rede-área, sendo estas direcionadas pela presença e/ou ausência das espécies remanescentes bem como das interações que estas realizam.


2015 ◽  
Vol 12 (11) ◽  
pp. 8497-8571 ◽  
Author(s):  
M. Portail ◽  
K. Olu ◽  
E. Escobar-Briones ◽  
J. C. Caprais ◽  
L. Menot ◽  
...  

Abstract. Understanding the ecological processes and connectivity of chemosynthetic deep-sea ecosystems requires comparative studies. In the Guaymas Basin (Gulf of California, Mexico), the presence of seeps and vents in the absence of biogeographic barrier, comparable sedimentary settings and depths offers a unique opportunity to assess the role of ecosystem specific environmental conditions on macrofaunal communities. Six seep and four vent assemblages were studied, three of which were characterised by common major foundation taxa: vesicomyid bivalves, siboglinid tubeworms and microbial mats. Macrofaunal community structure at the family level showed that density, diversity and composition patterns were primarily shaped by seep and vent common abiotic factors including methane and hydrogen sulphide concentrations. The type of substratum and the heterogeneity provided by foundation species were identified as additional structuring factors and their roles were found to vary according to fluid regimes. Surprisingly, the presence of vent environmental specificities, with higher temperature, higher metal concentrations and lower pH was not significant in explaining community patterns. Moreover, Guaymas seep and vent shared an important number of common species suggesting frequent connections between the two ecosystems. Finally, this study provides further support for the hypothesis of continuity among deep-sea seep and vent ecosystems.


2018 ◽  
Vol 115 (10) ◽  
pp. 2419-2424 ◽  
Author(s):  
Dirk Sanders ◽  
Elisa Thébault ◽  
Rachel Kehoe ◽  
F. J. Frank van Veen

Current species extinction rates are at unprecedentedly high levels. While human activities can be the direct cause of some extinctions, it is becoming increasingly clear that species extinctions themselves can be the cause of further extinctions, since species affect each other through the network of ecological interactions among them. There is concern that the simplification of ecosystems, due to the loss of species and ecological interactions, increases their vulnerability to such secondary extinctions. It is predicted that more complex food webs will be less vulnerable to secondary extinctions due to greater trophic redundancy that can buffer against the effects of species loss. Here, we demonstrate in a field experiment with replicated plant-insect communities, that the probability of secondary extinctions is indeed smaller in food webs that include trophic redundancy. Harvesting one species of parasitoid wasp led to secondary extinctions of other, indirectly linked, species at the same trophic level. This effect was markedly stronger in simple communities than for the same species within a more complex food web. We show that this is due to functional redundancy in the more complex food webs and confirm this mechanism with a food web simulation model by highlighting the importance of the presence and strength of trophic links providing redundancy to those links that were lost. Our results demonstrate that biodiversity loss, leading to a reduction in redundant interactions, can increase the vulnerability of ecosystems to secondary extinctions, which, when they occur, can then lead to further simplification and run-away extinction cascades.


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