iNAP: An integrated network analysis pipeline for microbiome studies

iMeta, Journal Year: 2022, Volume and Issue: 1(2)

Published: March 16, 2022

Abstract Integrated network analysis pipeline (iNAP) is an online for generating and analyzing comprehensive ecological networks in microbiome studies. It implemented two sections, that is, construction analysis, integrates many open‐access tools. Network contains multiple feasible alternatives, including correlation‐based approaches (Pearson's correlation Spearman's rank along with random matrix theory, sparse correlations compositional data) conditional dependence‐based methods (extended local similarity inverse covariance estimation association inference), while provides topological structures at different levels the potential effects of environmental factors on structures. Considering full workflow, from data set to result, iNAP molecular interdomain (IDENAP), which correspond intradomain associations microbial species taxonomic levels. Here, we describe detailed workflow by taking IDENAP as example show steps assist researchers conduct relevant analyses using their own sets. Afterwards, some auxiliary tools facilitating are introduced effectively aid switch operations. Therefore, iNAP, easy‐to‐use platform network‐associated approaches, can enable better understand organization communities. available http://mem.rcees.ac.cn:8081 free registration.

Language: Английский

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Passive acoustic monitoring provides a fresh perspective on fundamental ecological questions

Functional Ecology, Journal Year: 2023, Volume and Issue: 37(4), P. 959 - 975

Published: Jan. 20, 2023

Abstract Passive acoustic monitoring (PAM) has emerged as a transformative tool for applied ecology, conservation and biodiversity monitoring, but its potential contribution to fundamental ecology is less often discussed, PAM studies tend be descriptive, rather than mechanistic. Here, we chart the most promising directions ecologists wishing use suite of currently available methods address long‐standing questions in explore new avenues research. In both terrestrial aquatic habitats, provides an opportunity ask across multiple spatial scales at fine temporal resolution, capture phenomena or species that are difficult observe. combination with traditional approaches data collection, could release from myriad limitations have, times, precluded mechanistic understanding. We discuss several case demonstrate estimation, population trend analysis, assessing climate change impacts on phenology distribution, understanding disturbance recovery dynamics. also highlight what horizon PAM, terms near‐future technological methodological developments have provide advances coming years. Overall, illustrate how can harness power ecological era no longer characterised by limitation. Read free Plain Language Summary this article Journal blog.

Language: Английский

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Mutilation of the tree of life via mass extinction of animal genera

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(39)

Published: Sept. 18, 2023

Mass extinctions during the past 500 million y rapidly removed branches from phylogenetic tree of life and required millions years for evolution to generate functional replacements extinct (EX) organisms. Here we show, by examining 5,400 vertebrate genera (excluding fishes) comprising 34,600 species, that 73 became EX since 1500 AD. Beyond any doubt, human-driven sixth mass extinction is more severe than previously assessed accelerating. The current generic rates are 35 times higher expected background prevailing in last under absence human impacts. lost five centuries would have taken some 18,000 vanish beings. Current will likely greatly accelerate next few decades due drivers accompanying growth consumption enterprise such as habitat destruction, illegal trade, climate disruption. If all now-endangered were 2,100, be 354 (average) or 511 (for mammals) rates, meaning three 106,000 153,000 become humans. Such mutilation resulting loss ecosystem services provided biodiversity humanity a serious threat stability civilization. Immediate political, economic, social efforts an unprecedented scale essential if prevent these their societal

Language: Английский

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Biodiversity-friendly practices to support urban nature across ecosystem levels in green areas at different scales

Urban forestry & urban greening, Journal Year: 2025, Volume and Issue: unknown, P. 128682 - 128682

Published: Jan. 1, 2025

Language: Английский

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Universal scaling of robustness of ecosystem services to species loss

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Aug. 27, 2021

Abstract Ensuring reliable supply of services from nature is key to the sustainable development and well-being human societies. Varied frequently complex relationships between biodiversity ecosystem have, however, frustrated our capacity quantify predict vulnerability those species extinctions. Here, we use a qualitative Boolean modelling framework identify universal drivers robustness service loss. These comprise simple features networks that link functions they perform that, in turn, underpin service. Together, define what call network fragility. Using data >250 real ecological representing such as pollination seed-dispersal, demonstrate fragility predicts remarkably well empirical services. We then show how contributions individual robustness, enabling quantification scales Our findings provide general insights into way species, functional traits, links them together determine

Language: Английский

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Linking animal behavior to ecosystem change in disturbed environments

Frontiers in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 10

Published: July 14, 2022

Environmental disturbances often cause individuals to change their behavior. The behavioral responses can induce a chain of reactions through the network species interactions, via consumptive and trait mediated connections. Given that interactions define ecosystem structure functioning, changes these have ecological repercussions. Here, we explore transmission how influence conditions. We describe underlying mechanisms ultimate impact on including biodiversity ecosystems stability services. explain why some larger than others ecosystems, research should focus interactions. With work, synthesize existing theory empirical evidence provide conceptual framework links behavior altered community dynamics, processes. Considering link deeper understanding causes consequences improve our knowledge pathways which human activities alter ecosystems. This ability predict effects ongoing communities decide interventions needed mitigate negative effects.

Language: Английский

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How to measure response diversity

Methods in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 14(5), P. 1150 - 1167

Published: March 21, 2023

Abstract The insurance effect of biodiversity—that diversity stabilises aggregate ecosystem properties—is mechanistically underlain by inter‐ and intraspecific trait variation in organismal responses to the environment. This variation, termed response , is therefore a potentially critical determinant ecological stability. However, has yet be widely quantified, possibly due difficulties its measurement. Even when it been measured, approaches have varied. Here, we review methods for measuring from them distil methodological framework quantifying experimental and/or observational data, which can practically applied laboratory field settings across range taxa. Previous empirical studies on most commonly invoke traits as proxies aimed at capturing species' Our approach, based environment‐dependent any biotic or abiotic environmental variable, conceptually simple robust form response, including nonlinear responses. Given derivation data responses, this approach should more directly reflect than trait‐based dominant literature. By even subtle environment dependencies diversity, hope will motivate tests diversity–stability relationship new perspective, provide an mapping, monitoring conserving dimension biodiversity.

Language: Английский

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Biodiversity mitigates trade‐offs among species functional traits underpinning multiple ecosystem services

Ecology Letters, Journal Year: 2023, Volume and Issue: 26(6), P. 929 - 941

Published: April 6, 2023

Biodiversity loss and its effects on humanity is of major global concern. While a growing body literature confirms positive relationships between biodiversity multiple ecological functions, the links biodiversity, functions ecosystem services yet unclear. Studies biodiversity-functionality are mainly based computer simulations or controlled field experiments using only few species. Here, we use trait-based approach to integrate plant into an service assessment address impacts restoration species-rich grasslands over time. We found trade-offs among when analysing contributions from individual At community level, these disappeared for almost all with time since as effect increased species diversity more evenly distributed Restoration enhance also in communities therefore essential secure higher functional redundancy towards disturbances sustainable provision

Language: Английский

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An empirical assessment of whether urban green ecological networks have the capacity to store higher levels of carbon

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Feb. 7, 2024

Abstract Carbon–neutral growth is a crucial long-term climatic aim in the context of global warming. This paper introduces complex network theory and explores its potential application to achieve this goal. Specifically, we investigate spatial temporal distribution nodes sources ecological network, examine whether relationship exists between topological index landscape pattern source areas. We also determine contribution carbon stock entire by exploring correlation develop an optimization strategy based on synergistic effect node-source enhancement. Finally, test through robustness. Our results show that: (1) The feature analysis reveals that degree node network's characteristics becomes dispersed modular, exhibiting small-world networks according large clustering coefficient. heterogeneity extent landscapes have increased modularity but remain distributed locally fragmented; (2) According analysis, enhancing eccentricity topology, patch cohesion (COHESION) site can maximize enhancement benefits site; (3) tests robustness edges links, stability improved sink capacity enhanced. Simultaneously, restoration rejuvenation space national construction projects effectively improve within organized region, contributing neutrality aim. research gives scientific quantifiable references for sustainable cities urban structure.

Language: Английский

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Linking network ecology and ecosystem services to benefit people

People and Nature, Journal Year: 2024, Volume and Issue: 6(3), P. 1048 - 1059

Published: March 22, 2024

Abstract Ecosystems are rapidly degraded by anthropogenic pressures, affecting the provision of ecosystem services. Therefore, it is increasingly important that we can quantify and manage services to maintain human well‐being. Many underpinned functions processes driven interspecific ecological interactions. Humans then benefit from through socio‐ecological interaction network approaches provide a unique understanding service flows. In this paper, assess current interface between ecology services, before exploring how work linking these two fields could be enhanced. We emphasise value explore methods improve assessment management Within this, highlight role local indigenous knowledge in operationalising useful context. Read free Plain Language Summary for article on Journal blog.

Language: Английский

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