scholarly journals Toward a Better Understanding of Species Interactions through Network Biology

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Ryan S. McClure
Keyword(s):  
Complex Systems ◽  
Species Interactions ◽  
Omics Data ◽  
New Methods ◽  
Strong Position ◽  
Multiple Species ◽  
Network Approaches ◽  
Natural Settings ◽  
Microbial Systems ◽  
Omic Data

ABSTRACT Within the last decade, there has been an explosion of multi-omics data generated for several microbial systems. At the same time, new methods of analysis have emerged that are based on inferring networks that link features both within and between species based on correlation in abundance. These developments prompt two important questions. What can be done with network approaches to better understand microbial species interactions? What challenges remain in applying network approaches to query the more complex systems of natural settings? Here, I briefly describe what has been done and what questions still need to be answered. Over the next 5 to 10 years, we will be in a strong position to infer networks that contain multiple kinds of omic data and describe systems with multiple species. These applications will open the door for a better understanding and use of microbiomes across a variety of fields.

scholarly journals Genetic identity and genotype × genotype interactions between symbionts outweigh species level effects in an insect microbiome

2021 ◽  
Author(s):  
Melanie R. Smee ◽  
Sally A. Raines ◽  
Julia Ferrari
Keyword(s):  
Species Interactions ◽  
Acyrthosiphon Pisum ◽  
Parasitoid Wasp ◽  
Extensive Study ◽  
Genetic Identity ◽  
Host Genotype ◽  
Species Identity ◽  
Microbial Symbionts ◽  
And Performance ◽  
Multiple Species

AbstractMicrobial symbionts often alter the phenotype of their host. Benefits and costs to hosts depend on many factors, including host genotype, symbiont species and genotype, and environmental conditions. Here, we present a study demonstrating genotype-by-genotype (G×G) interactions between multiple species of endosymbionts harboured by an insect, and the first to quantify the relative importance of G×G interactions compared with species interactions in such systems. In the most extensive study to date, we microinjected all possible combinations of five Hamiltonella defensa and five Fukatsuia symbiotica (X-type; PAXS) isolates into the pea aphid, Acyrthosiphon pisum. We applied several ecological challenges: a parasitoid wasp, a fungal pathogen, heat shock, and performance on different host plants. Surprisingly, genetic identity and genotype × genotype interactions explained far more of the phenotypic variation (on average 22% and 31% respectively) than species identity or species interactions (on average 12% and 0.4%, respectively). We determined the costs and benefits associated with co-infection, and how these compared to corresponding single infections. All phenotypes were highly reliant on individual isolates or interactions between isolates of the co-infecting partners. Our findings highlight the importance of exploring the eco-evolutionary consequences of these highly specific interactions in communities of co-inherited species.

scholarly journals Evaluating Coexistence of Fish Species with Coastal Cutthroat Trout in Low Order Streams of Western Oregon and Washington, USA

Fishes ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 4
Author(s):  
Kyle D. Martens ◽  
Jason Dunham
Keyword(s):  
Pacific Northwest ◽  
Species Interactions ◽  
Coho Salmon ◽  
Cutthroat Trout ◽  
Single Species ◽  
The Pacific ◽  
Small Streams ◽  
Coastal Cutthroat Trout ◽  
Multiple Species ◽  
Low Order

When multiple species of fish coexist there are a host of potential ways through which they may interact, yet there is often a strong focus on studies of single species without considering these interactions. For example, many studies of forestry–stream interactions in the Pacific Northwest have focused solely on the most prevalent species: Coastal cutthroat trout. To examine the potential for interactions of other fishes with coastal cutthroat trout, we conducted an analysis of 281 sites in low order streams located on Washington’s Olympic Peninsula and along the central Oregon coast. Coastal cutthroat trout and juvenile coho salmon were the most commonly found salmonid species within these streams and exhibited positive associations with each other for both presence and density. Steelhead were negatively associated with the presence of coastal cutthroat trout as well as with coho salmon and sculpins (Cottidae). Coastal cutthroat trout most frequently shared streams with juvenile coho salmon. For densities of these co-occurring species, associations between these two species were relatively weak compared to the strong influences of physical stream conditions (size and gradient), suggesting that physical conditions may have more of an influence on density than species interactions. Collectively, our analysis, along with a review of findings from prior field and laboratory studies, suggests that the net effect of interactions between coastal cutthroat trout and coho salmon do not appear to inhibit their presence or densities in small streams along the Pacific Northwest.

scholarly journals Pathway and Network Approaches for Identification of Cancer Signature Markers from Omics Data

2015 ◽  
Vol 6 (1) ◽  
pp. 54-65 ◽  
Author(s):  
Jinlian Wang ◽  
Yiming Zuo ◽  
Yan-gao Man ◽  
Itzhak Avital ◽  
Alexander Stojadinovic ◽  
...  
Keyword(s):  
Omics Data ◽  
Network Approaches

scholarly journals The new big picture for linguistics: Complex systems

2018 ◽  
Vol 4 (1) ◽  
pp. 1-20
Author(s):  
William A. Kretzschmar
Keyword(s):  
Complex Systems ◽  
Distributional Pattern ◽  
Logical System ◽  
Human Speech ◽  
New Methods ◽  
Central Factor ◽  
History Of Linguistics ◽  
Big Picture ◽  
History Of ◽  
Logical Nature

Abstract In the history of linguistics there have been crucial moments when those of us interested in language have essentially changed the way we study our subject. We stand now at such a moment. In this presentation I will review the history of linguistics in order to highlight some past important changes in the field, and then turn to where we stand now. Some things that we thought we knew have turned out not to be true, like the systematic, logical nature of languages. Other things that we had not suspected, like a universal underlying emergent pattern for all the features of a language, are now evident. This emergent pattern is fractal, that is, we can observe the same distributional pattern in frequency profiles for linguistic variants at every level of scale in our analysis. We also have hints that time, as the persistence of a preference for particular variants of features, is a much more important part of our language than we had previously believed. We need to explore the new realities of language as we now understand them, chief among them the idea that patterned variation, not logical system, is the central factor in human speech. In order to account for what we now understand, we need to get used to new methods of study and presentation, and place new emphasis on different communities and groups of speakers. Because the underlying pattern of language is fractal, we need to examine the habits of every group of speakers at every location for themselves, as opposed to our previous emphasis on overall grammars. We need to make our studies much more local, as opposed to global. We do still want to make grammars and to understand language in global terms, but such generalizations need to follow from what we can now see as the pattern of language as it is actually used.

How a network approach has advanced the field of plant invasion ecology.

2020 ◽  
pp. 324-339
Author(s):  
Carine Emer ◽  
◽  
Sérgio Timóteo ◽  
◽  
Keyword(s):  
Species Interactions ◽  
Plant Invasion ◽  
Native Species ◽  
Invasion Biology ◽  
Plant Invasions ◽  
Network Approach ◽  
Native Plant Species ◽  
Functional Roles ◽  
Network Approaches ◽  
Plant Herbivore

Every organism on Earth, whether in natural or anthropogenic environments, is connected to a complex web of life, the famous 'entangled bank' coined by Darwin in 1859. Non-native species can integrate into local 'banks' by establishing novel associations with the resident species. In that context, network ecology has been an important tool to study the interactions of non-native species and the effects on recipient communities due to its ability to simultaneously investigate the assembly and disassembly of species interactions as well as their functional roles. Its visually appealing tools and relatively simple metrics gained momentum among scientists and are increasingly applied in different areas of ecology, from the more theoretical grounds to applied research on restoration and conservation. A network approach helps us to understand how plant invasions may or may not form novel species associations, how they change the structure of invaded communities, the outcomes for ecosystem functionality and, ultimately, the implications for the conservation of ecological interactions. Networks have been widely used on pollination studies, especially from temperate zones, unveiling their nested patterns and the mechanisms by which non-native plants integrate into local communities. Yet, very few papers have used network approaches to assess plant invasion effects in other systems such as plant-herbivore, plant-pathogen or seed-dispersal processes. Here we describe how joining network ecology with plant invasion biology started and how it has developed over the last few decades. We show the extent of its contribution, despite contradictory results and biases, to a better understanding of the role of non-native plant species in shaping community structure. Finally, we explore how it can be further improved to answer emerging questions.

scholarly journals Aridity weakens population-level effects of multiple species interactions on Hibiscus meyeri

2017 ◽  
Vol 115 (3) ◽  
pp. 543-548 ◽  
Author(s):  
Allison M. Louthan ◽  
Robert M. Pringle ◽  
Jacob R. Goheen ◽  
Todd M. Palmer ◽  
William F. Morris ◽  
...  
Keyword(s):  
Population Growth ◽  
Species Interactions ◽  
Abiotic Factors ◽  
Population Level ◽  
Distinct Species ◽  
High Elevation ◽  
Relative Strength ◽  
Herbaceous Plant ◽  
Species Abundances ◽  
Multiple Species

Predicting how species’ abundances and ranges will shift in response to climate change requires a mechanistic understanding of how multiple factors interact to limit population growth. Both abiotic stress and species interactions can limit populations and potentially set range boundaries, but we have a poor understanding of when and where each is most critical. A commonly cited hypothesis, first proposed by Darwin, posits that abiotic factors (e.g., temperature, precipitation) are stronger determinants of range boundaries in apparently abiotically stressful areas (“stress” indicates abiotic factors that reduce population growth), including desert, polar, or high-elevation environments, whereas species interactions (e.g., herbivory, competition) play a stronger role in apparently less stressful environments. We tested a core tenet of this hypothesis—that population growth rate is more strongly affected by species interactions in less stressful areas—using experimental manipulations of species interactions affecting a common herbaceous plant, Hibiscus meyeri (Malvaceae), across an aridity gradient in a semiarid African savanna. Population growth was more strongly affected by four distinct species interactions (competition with herbaceous and shrubby neighbors, herbivory, and pollination) in less stressful mesic areas than in more stressful arid sites. However, contrary to common assumptions, this effect did not arise because of greater density or diversity of interacting species in less stressful areas, but rather because aridity reduced sensitivity of population growth to these interactions. Our work supports classic predictions about the relative strength of factors regulating population growth across stress gradients, but suggests that this pattern results from a previously unappreciated mechanism that may apply to many species worldwide.

scholarly journals Cross-Species Transmission of Coronaviruses in Humans and  Domestic Mammals, What Are the Ecological Mechanisms Driving Transmission, Spillover,  and Disease Emergence?

2021 ◽  
Author(s):  
Nicole Nova
Keyword(s):  
Host Range ◽  
Host Species ◽  
Species Interactions ◽  
Host Density ◽  
Mammalian Host ◽  
The Novel ◽  
Disease Emergence ◽  
Short Period ◽  
Rapid Diversification ◽  
Multiple Species

Coronaviruses cause respiratory and digestive diseases in vertebrates. The recent pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2, is taking a heavy toll on society and planetary health, and illustrates the threat emerging coronaviruses can pose to the wellbeing of humans and other animals. Coronaviruses are constantly evolving, crossing host species barriers, and expanding their host range. In the last few decades, several novel coronaviruses have emerged in humans and domestic animals. Novel coronaviruses have also been discovered in captive wildlife or wild populations, raising conservation concerns. The evolution and emergence of novel viruses is enabled by frequent cross-species transmission. It is thus crucial to determine emerging coronaviruses’ potential for infecting different host species, and to identify the circumstances under which cross-species transmission occurs in order to mitigate the rate of disease emergence. Here, I review (broadly across several mammalian host species) up-to-date knowledge of host range and circumstances concerning reported cross-species transmission events of emerging coronaviruses in humans and common domestic mammals. All of these coronaviruses had similar host ranges, were closely related (indicative of rapid diversification and spread), and their emergence was likely associated with high-host-density environments facilitating multi-species interactions (e.g., shelters, farms, and markets) and the health or wellbeing of animals as end- and/or intermediate spillover hosts. Further research is needed to identify mechanisms of the cross-species transmission events that have ultimately led to a surge of emerging coronaviruses in multiple species in a relatively short period of time in a world undergoing rapid environmental change.

scholarly journals Formation, Development, and Cross-Species Interactions in Biofilms

2022 ◽  
Vol 12 ◽  
Author(s):  
Aihua Luo ◽  
Fang Wang ◽  
Degang Sun ◽  
Xueyu Liu ◽  
Bingchang Xin
Keyword(s):  
Species Interactions ◽  
Bacterial Infections ◽  
Early Stage ◽  
Microbial Interactions ◽  
Bacterial Survival ◽  
Chronic Infections ◽  
Immune Attack ◽  
Biofilm Development ◽  
Natural Settings ◽  
Harmful Effects

Biofilms, which are essential vectors of bacterial survival, protect microbes from antibiotics and host immune attack and are one of the leading causes that maintain drug-resistant chronic infections. In nature, compared with monomicrobial biofilms, polymicrobial biofilms composed of multispecies bacteria predominate, which means that it is significant to explore the interactions between microorganisms from different kingdoms, species, and strains. Cross-microbial interactions exist during biofilm development, either synergistically or antagonistically. Although research into cross-species biofilms remains at an early stage, in this review, the important mechanisms that are involved in biofilm formation are delineated. Then, recent studies that investigated cross-species cooperation or synergy, competition or antagonism in biofilms, and various components that mediate those interactions will be elaborated. To determine approaches that minimize the harmful effects of biofilms, it is important to understand the interactions between microbial species. The knowledge gained from these investigations has the potential to guide studies into microbial sociality in natural settings and to help in the design of new medicines and therapies to treat bacterial infections.

scholarly journals Improving stability of prediction models based on correlated omics data by using network approaches

PLoS ONE ◽  
2018 ◽  
Vol 13 (2) ◽  
pp. e0192853 ◽  
Author(s):  
Renaud Tissier ◽  
Jeanine Houwing-Duistermaat ◽  
Mar Rodríguez-Girondo
Keyword(s):  
Prediction Models ◽  
Omics Data ◽  
Network Approaches

Computational Approaches Leveraging Integrated Connections of Multi-Omic Data toward Clinical Applications

2021 ◽  
Author(s):  
Cansu H Demirel ◽  
Kaan M Arici ◽  
Nurcan Tuncbag
Keyword(s):  
High Throughput ◽  
Biological Systems ◽  
Clinical Applications ◽  
Data Type ◽  
Omics Data ◽  
Computational Approaches ◽  
Omic Data

In line with the advances in high-throughput technologies, multiple omic datasets have accumulated to study biological systems and diseases coherently. No single omics data type is capable of fully representing...

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