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https://www.readbyqxmd.com/read/29158553/the-architecture-of-mutualistic-networks-as-an-evolutionary-spandrel
#1
Sergi Valverde, Jordi Piñero, Bernat Corominas-Murtra, Jose Montoya, Lucas Joppa, Ricard Solé
Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species, including a widespread presence of nestedness. The nested structure of these webs seems to be positively correlated with higher diversity and resilience. Moreover, these webs exhibit marked measurable structural patterns, including broad distributions of connectivity, strongly asymmetrical interactions and hierarchical organization. Hierarchical organization is an especially interesting property, since it is positively correlated with biodiversity and network resilience, thus suggesting potential selection processes favouring the observed web organization...
November 20, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29133886/disentangling-the-co-structure-of-multilayer-interaction-networks-degree-distribution-and-module-composition-in-two-layer-bipartite-networks
#2
Julia Astegiano, Florian Altermatt, François Massol
Species establish different interactions (e.g. antagonistic, mutualistic) with multiple species, forming multilayer ecological networks. Disentangling network co-structure in multilayer networks is crucial to predict how biodiversity loss may affect the persistence of multispecies assemblages. Existing methods to analyse multilayer networks often fail to consider network co-structure. We present a new method to evaluate the modular co-structure of multilayer networks through the assessment of species degree co-distribution and network module composition...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133453/expanding-the-informational-chemistries-of-life-peptide-rna-networks
#3
REVIEW
Olga Taran, Chenrui Chen, Tolulope O Omosun, Ming-Chien Hsieh, Allisandra Rha, Jay T Goodwin, Anil K Mehta, Martha A Grover, David G Lynn
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29131838/expanded-repertoire-of-kinetoplast-associated-proteins-and-unique-mitochondrial-dna-arrangement-of-symbiont-bearing-trypanosomatids
#4
Silvana Sant Anna de Souza, Carolina Moura Catta-Preta, João Marcelo P Alves, Danielle P Cavalcanti, Marta M G Teixeira, Erney P Camargo, Wanderley De Souza, Rosane Silva, Maria Cristina M Motta
In trypanosomatids, the kinetoplast is the portion of the single mitochondrion that is connected to the basal body and contains the kDNA, a network composed by circular and interlocked DNA. The kDNA packing is conducted by Kinetoplast Associated Proteins (KAPs), which are similar to eukaryotic histone H1. In symbiont-harboring trypanosomatids (SHTs) such as Angomonas deanei and Strigomonas culicis, a ß-proteobacterium co-evolves with the host in a mutualistic relationship. The prokaryote confers nutritional benefits to the host and affects its cell structure...
2017: PloS One
https://www.readbyqxmd.com/read/29082521/interaction-frequency-network-position-and-the-temporal-persistence-of-interactions-in-a-plant-pollinator-network
#5
Natacha P Chacoff, Julian Resasco, Diego P Vázquez
Ecological interactions are highly dynamic in time and space. Previous studies of plant-animal mutualistic networks have shown that the occurrence of interactions varies substantially across years. We analyzed inter-annual variation of a quantitative mutualistic network, in which links are weighted by interaction frequency. The network was sampled over six consecutive years, representing one of the longest time series for a community-wide mutualistic network. We estimated the inter-annual similarity in interactions and assessed the determinants of their persistence...
October 30, 2017: Ecology
https://www.readbyqxmd.com/read/29045396/indirect-effects-drive-coevolution-in-mutualistic-networks
#6
Paulo R Guimarães, Mathias M Pires, Pedro Jordano, Jordi Bascompte, John N Thompson
Ecological interactions have been acknowledged to play a key role in shaping biodiversity. Yet a major challenge for evolutionary biology is to understand the role of ecological interactions in shaping trait evolution when progressing from pairs of interacting species to multispecies interaction networks. Here we introduce an approach that integrates coevolutionary dynamics and network structure. Our results show that non-interacting species can be as important as directly interacting species in shaping coevolution within mutualistic assemblages...
October 26, 2017: Nature
https://www.readbyqxmd.com/read/29024173/root-transcriptional-dynamics-induced-by-beneficial-rhizobacteria-and-microbial-immune-elicitors-reveal-signatures-of-adaptation-to-mutualists
#7
Ioannis A Stringlis, Silvia Proietti, Richard Hickman, Marcel C Van Verk, Christos Zamioudis, Corné M J Pieterse
Belowground, microbe-associated molecular patterns (MAMPs) of root-associated microbiota can trigger costly defenses at the expense of plant growth. However, beneficial rhizobacteria, such as Pseudomonas simiae WCS417, promote plant growth and induce systemic resistance without being warded off by local root immune responses. To investigate early root responses that facilitate WCS417 to exert its plant-beneficial functions, we performed time-series RNA-Seq of Arabidopsis roots in response to live WCS417 and compared it to MAMPs flg22(417) (from WCS417), flg22(Pa) (from pathogenic Pseudomonas aeruginosa), and fungal chitin...
October 10, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28970589/network-structure-embracing-mutualism-antagonism-continuums-increases-community-robustness
#8
Alicia Montesinos-Navarro, Fernando Hiraldo, José L Tella, Guillermo Blanco
Theory predicts that contrasting properties of mutualistic and antagonistic networks differentially promote community resilience to species loss. However, the outcome of most ecological interactions falls within a continuum between mutualism and antagonism, and we ignore the extent to which this interactions' continuum might influence community stability. Using a large data set of interactions, we compared co-extinction cascades that either consider or ignore the mix of beneficial and detrimental actions that parrots exert on plants...
October 2, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28941124/comparing-species-interaction-networks-along-environmental-gradients
#9
Loïc Pellissier, Camille Albouy, Jordi Bascompte, Nina Farwig, Catherine Graham, Michel Loreau, Maria Alejandra Maglianesi, Carlos J Melián, Camille Pitteloud, Tomas Roslin, Rudolf Rohr, Serguei Saavedra, Wilfried Thuiller, Guy Woodward, Niklaus E Zimmermann, Dominique Gravel
Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions...
September 22, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28923004/regulatory-networks-underlying-mycorrhizal-development-delineated-by-genome-wide-expression-profiling-and-functional-analysis-of-the-transcription-factor-repertoire-of-the-plant-symbiotic-fungus-laccaria-bicolor
#10
Y Daguerre, E Levati, J Ruytinx, E Tisserant, E Morin, A Kohler, B Montanini, S Ottonello, A Brun, C Veneault-Fourrey, F Martin
BACKGROUND: Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28911664/smog-induces-oxidative-stress-and-microbiota-disruption
#11
REVIEW
Tit-Yee Wong
Smog is created through the interactions between pollutants in the air, fog, and sunlight. Air pollutants, such as carbon monoxide, heavy metals, nitrogen oxides, ozone, sulfur dioxide, volatile organic vapors, and particulate matters, can induce oxidative stress in human directly or indirectly through the formation of reactive oxygen species. The outermost boundary of human skin and mucous layers are covered by a complex network of human-associated microbes. The relation between these microbial communities and their human host are mostly mutualistic...
April 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28900208/qualitative-and-quantitative-responses-to-press-perturbations-in-ecological-networks
#12
Giulia Giordano, Claudio Altafini
Predicting the sign of press perturbation responses in ecological networks is challenging, due to the poor knowledge of the strength of the direct interactions among the species, and to the entangled coexistence of direct and indirect effects. We show in this paper that, for a class of networks that includes mutualistic and monotone networks, the sign of press perturbation responses can be qualitatively determined based only on the sign pattern of the community matrix, without any knowledge of parameter values...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886540/paddy-soil-microbial-communities-driven-by-environment-and-microbe-microbe-interactions-a-case-study-of-elevation-resolved-microbial-communities-in-a-rice-terrace
#13
Weimin Sun, Enzong Xiao, Zilun Pu, Valdis Krumins, Yiran Dong, Baoqin Li, Min Hu
Rice paddies are a significant source of the greenhouse gas methane, which mainly originates from microbial activity. Methane generation in anaerobic systems involves complex interactions of multiple functional microbial groups. Rice paddies installed in hilly terrain are often terraced, providing multiple quasi-independent plots differing primarily in their elevation up a hillside. This represents an excellent study site to explore the influence of environmental factors on microbial communities and interactions among microbial populations...
January 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/28852574/spatially-induced-nestedness-in-a-neutral-model-of-phage-bacteria-networks
#14
Sergi Valverde, Santiago F Elena, Ricard Solé
Ecological networks, both displaying mutualistic or antagonistic interactions, seem to share common structural traits: the presence of nestedness and modularity. A variety of model approaches and hypothesis have been formulated concerning the significance and implications of these properties. In phage-bacteria bipartite infection networks, nestedness seems to be the rule in many different contexts. Modeling the coevolution of a diverse virus-host ensemble is a difficult task, given the dimensionality and multi parametric nature of a standard continuous approximation...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/28846734/identifying-species-at-coextinction-risk-when-detection-is-imperfect-model-evaluation-and-case-study
#15
Michaela Plein, William K Morris, Melinda L Moir, Peter A Vesk
Losing a species from a community can cause further extinctions, a process also known as coextinction. The risk of being extirpated with an interaction partner is commonly inferred from a species' host-breadth, derived from observing interactions between species. But observational data suffers from imperfect detection, making coextinction estimates highly unreliable. To address this issue and to account for data uncertainty, we fit a hierarchical N-mixture model to individual-level interaction data from a mutualistic network...
2017: PloS One
https://www.readbyqxmd.com/read/28833083/why-are-some-plant-pollinator-networks-more-nested-than-others
#16
Chuliang Song, Rudolf P Rohr, Serguei Saavedra
Empirical studies have found that the mutualistic interactions forming the structure of plant-pollinator networks are typically more nested than expected by chance alone. Additionally, theoretical studies have shown a positive association between the nested structure of mutualistic networks and community persistence. Yet, it has been shown that some plant-pollinator networks may be more nested than others, raising the interesting question of which factors are responsible for such enhanced nested structure. It has been argued that ordered network structures may increase the persistence of ecological communities under less predictable environments...
October 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28829637/ants-at-plant-wounds-a-little-known-trophic-interaction-with-evolutionary-implications-for-ant-plant-interactions
#17
Michael Staab, Felix Fornoff, Alexandra-Maria Klein, Nico Blüthgen
Extrafloral nectaries (EFNs) allow plants to engage in mutualisms with ants, preventing herbivory in exchange for food. EFNs occur scattered throughout the plant phylogeny and likely evolved independent from herbivore-created wounds subsequently visited by ants collecting leaked sap. Records of wound-feeding ants are, however, anecdotal. By surveying 38,000 trees from 40 species, we conducted the first quantitative ecological study of this overlooked behavior. Ant-wound interactions were widespread (0.5% of tree individuals) and occurred on 23 tree species...
September 2017: American Naturalist
https://www.readbyqxmd.com/read/28812626/dispersal-governs-the-reorganization-of-ecological-networks-under-environmental-change
#18
Patrick L Thompson, Andrew Gonzalez
Ecological networks, such as food webs, mutualist webs and host-parasite webs, are reorganizing as species abundances and spatial distributions shift in response to environmental change. Current theoretical expectations for how this reorganization will occur are available for competition or for parts of interaction networks, but these may not extend to more complex networks. Here we use metacommunity theory to develop new expectations for how complex networks will reorganize under environmental change, and show that dispersal is crucial for determining the degree to which networks will retain their composition and structure...
May 8, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28810707/seasonal-and-spatial-variations-of-prokaryoplankton-communities-in-a-salinity-influenced-watershed-china
#19
Anyi Hu, Hongjie Wang, Xiaoyang Yang, Liyuan Hou, Jiangwei Li, Shuang Li, Chang-Ping Yu
Prokaryotes represent the largest biodiversity pool and drive the biogeochemical cycles in fluvial environments. However, the mechanisms underlying the assembly of prokaryotic communities are largely unexplored at taxonomic and functional levels, simultaneously. Here, we investigated the spatio-seasonal distribution of prokaryoplankton communities in a salinity-influenced watershed, China using 16S rRNA gene amplicon sequencing. The OTUs were divided into core and satellite, based on a statistical approach...
August 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28754943/design-of-multi-phase-dynamic-chemical-networks
#20
Chenrui Chen, Junjun Tan, Ming-Chien Hsieh, Ting Pan, Jay T Goodwin, Anil K Mehta, Martha A Grover, David G Lynn
Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates...
August 2017: Nature Chemistry
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