1
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Damos PT. On formal limitations of causal ecological networks. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230170. [PMID: 39034692 PMCID: PMC11293863 DOI: 10.1098/rstb.2023.0170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/02/2023] [Accepted: 02/22/2024] [Indexed: 07/23/2024] Open
Abstract
Causal multivariate time-series analysis, combined with network theory, provide a powerful tool for studying complex ecological interactions. However, these methods have limitations often underestimated when used in graphical modelling of ecological systems. In this opinion article, I examine the relationship between formal logic methods used to describe causal networks and their inherent statistical and epistemological limitations. I argue that while these methods offer valuable insights, they are restricted by axiomatic assumptions, statistical constraints and the incompleteness of our knowledge. To prove that, I first consider causal networks as formal systems, define causality and formalize their axioms in terms of modal logic and use ecological counterexamples to question the axioms. I also highlight the statistical limitations when using multivariate time-series analysis and Granger causality to develop ecological networks, including the potential for spurious correlations among other data characteristics. Finally, I draw upon Gödel's incompleteness theorems to highlight the inherent limits of fully understanding complex networks as formal systems and conclude that causal ecological networks are subject to initial rules and data characteristics and, as any formal system, will never fully capture the intricate complexities of the systems they represent. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.
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Affiliation(s)
- Petros T. Damos
- Minstry of Education, Religious and Sports, Directorate of Secondary Education Veroia, Ergohori59132, Greece
- Department of Agriculture, School of Agricultural Studies, University of Western Macedonia, Florina, 53100, Greece
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Western Macedonia, Kozani50100, Greece
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2
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Tian L, Rao W, Zhao K, Vo HT. Analyzing world city network by graph convolutional networks. Sci Rep 2024; 14:18933. [PMID: 39147920 PMCID: PMC11327301 DOI: 10.1038/s41598-024-69494-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 08/05/2024] [Indexed: 08/17/2024] Open
Abstract
British scholar Peter Taylor constructed the World City Network by analyzing the office networks of multinational companies, enabling a network perspective on world cities. However, this method has long been hindered by data deficiencies and update delays. In this study, we utilized publicly available, real-time updated data on global routes to construct the World City Network, thereby addressing the issues of data insufficiency and delayed updates in the existing model. For the first time, advanced Graph Convolutional Networks were employed to analyze the World City Network, and we introduced GCNRank. Finally, we compared GCNRank with other centrality measures and found that GCNRank provides a more detailed representation of city rankings and effectively avoids local optima.
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Affiliation(s)
- Linfang Tian
- School of Software Engineering, Tongji University, Shanghai, 201804, China.
| | - Weixiong Rao
- School of Software Engineering, Tongji University, Shanghai, 201804, China
| | - Kai Zhao
- J. Mack Robinson College of Business, Georgia State University, Atlanta, 30301, USA
| | - Huy T Vo
- The City College of New York, City University of New York and New York University, New York, 10031, USA
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3
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Laine AL, Tylianakis JM. The coevolutionary consequences of biodiversity change. Trends Ecol Evol 2024; 39:745-756. [PMID: 38705768 DOI: 10.1016/j.tree.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/07/2024]
Abstract
Coevolutionary selection is a powerful process shaping species interactions and biodiversity. Anthropogenic global environmental change is reshaping planetary biodiversity, including by altering the structure and intensity of interspecific interactions. However, remarkably little is understood of how coevolutionary selection is changing in the process. Here, we outline three interrelated pathways - change in evolutionary potential, change in community composition, and shifts in interaction trait distributions - that are expected to redirect coevolutionary selection under biodiversity change. Assessing how both ecological and evolutionary rules governing species interactions are disrupted under anthropogenic global change is of paramount importance to understand the past, present, and future of Earth's biodiversity.
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Affiliation(s)
- Anna-Liisa Laine
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikinkaari 1 (PO Box 65), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Jason M Tylianakis
- Bioprotection Aotearoa, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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4
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Fouqueau L, Polechová J. Eco-evolutionary dynamics in changing environments: integrating theory with data. J Evol Biol 2024; 37:579-587. [PMID: 38941551 DOI: 10.1093/jeb/voae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Affiliation(s)
- Louise Fouqueau
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jitka Polechová
- Department of Mathematics, University of Vienna, Vienna, Austria
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5
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Mateos DM, Bhatnagar JM. Restoring ecological complexity in a changing environment. Curr Biol 2024; 34:R365-R371. [PMID: 38714167 DOI: 10.1016/j.cub.2024.03.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
As land use leaves massive tracts of land vacant for recovery, restoration must undergo a substantial shift to incorporate a complexity perspective beyond the traditional community, biodiversity or functional views. With an interaction-function perspective, we may be able to achieve ecosystems with better chances to adapt to current environmental changes and, especially, to climate change. We explore combined approaches that include still unused and underexplored techniques that will soon go mainstream and produce massive amounts of information to address the complexity gap. As we understand how complexity reassembles after the end of agriculture, we will be able to design actions to restore or enhance it at unprecedented spatial scales while increasing its adaptability to environmental changes.
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Affiliation(s)
- David Moreno Mateos
- School of Geography and the Environment, University of Oxford, Oxford OX1 3QY, UK; Basque Centre for Climate Change (BC3), Leioa 48940, Spain; Ikerbasque Foundation, Bilbao 48009, Spain.
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6
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Pontarp M, Runemark A, Friberg M, Opedal ØH, Persson AS, Wang L, Smith HG. Evolutionary plant-pollinator responses to anthropogenic land-use change: impacts on ecosystem services. Biol Rev Camb Philos Soc 2024; 99:372-389. [PMID: 37866400 DOI: 10.1111/brv.13026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
Agricultural intensification at field and landscape scales, including increased use of agrochemicals and loss of semi-natural habitats, is a major driver of insect declines and other community changes. Efforts to understand and mitigate these effects have traditionally focused on ecological responses. At the same time, adaptations to pesticide use and habitat fragmentation in both insects and flowering plants show the potential for rapid evolution. Yet we lack an understanding of how such evolutionary responses may propagate within and between trophic levels with ensuing consequences for conservation of species and ecological functions in agroecosystems. Here, we review the literature on the consequences of agricultural intensification on plant and animal evolutionary responses and interactions. We present a novel conceptualization of evolutionary change induced by agricultural intensification at field and landscape scales and emphasize direct and indirect effects of rapid evolution on ecosystem services. We exemplify by focusing on economically and ecologically important interactions between plants and pollinators. We showcase available eco-evolutionary theory and plant-pollinator modelling that can improve predictions of how agricultural intensification affects interaction networks, and highlight available genetic and trait-focused methodological approaches. Specifically, we focus on how spatial genetic structure affects the probability of propagated responses, and how the structure of interaction networks modulates effects of evolutionary change in individual species. Thereby, we highlight how combined trait-based eco-evolutionary modelling, functionally explicit quantitative genetics, and genomic analyses may shed light on conditions where evolutionary responses impact important ecosystem services.
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Affiliation(s)
- Mikael Pontarp
- Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Anna Runemark
- Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Magne Friberg
- Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Øystein H Opedal
- Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Anna S Persson
- Centre for Environmental and Climate Science (CEC), Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Lingzi Wang
- Centre for Environmental and Climate Science (CEC), Lund University, Sölvegatan 37, Lund, 22362, Sweden
- School of Mathematical Sciences, University of Southampton, 58 Salisbury Rd, Southampton, SO17 1BJ, UK
| | - Henrik G Smith
- Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
- Centre for Environmental and Climate Science (CEC), Lund University, Sölvegatan 37, Lund, 22362, Sweden
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7
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Cantwell-Jones A, Tylianakis JM, Larson K, Gill RJ. Using individual-based trait frequency distributions to forecast plant-pollinator network responses to environmental change. Ecol Lett 2024; 27:e14368. [PMID: 38247047 DOI: 10.1111/ele.14368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/23/2024]
Abstract
Determining how and why organisms interact is fundamental to understanding ecosystem responses to future environmental change. To assess the impact on plant-pollinator interactions, recent studies have examined how the effects of environmental change on individual interactions accumulate to generate species-level responses. Here, we review recent developments in using plant-pollinator networks of interacting individuals along with their functional traits, where individuals are nested within species nodes. We highlight how these individual-level, trait-based networks connect intraspecific trait variation (as frequency distributions of multiple traits) with dynamic responses within plant-pollinator communities. This approach can better explain interaction plasticity, and changes to interaction probabilities and network structure over spatiotemporal or other environmental gradients. We argue that only through appreciating such trait-based interaction plasticity can we accurately forecast the potential vulnerability of interactions to future environmental change. We follow this with general guidance on how future studies can collect and analyse high-resolution interaction and trait data, with the hope of improving predictions of future plant-pollinator network responses for targeted and effective conservation.
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Affiliation(s)
- Aoife Cantwell-Jones
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Jason M Tylianakis
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
- Bioprotection Aotearoa, School of Biological Sciences, Private Bag 4800, University of Canterbury, Christchurch, New Zealand
| | - Keith Larson
- Climate Impacts Research Centre, Department of Ecology and Environmental Sciences, Umeå University, Umeå, Sweden
| | - Richard J Gill
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
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8
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Graham NR, Krehenwinkel H, Lim JY, Staniczenko P, Callaghan J, Andersen JC, Gruner DS, Gillespie RG. Ecological network structure in response to community assembly processes over evolutionary time. Mol Ecol 2023; 32:6489-6506. [PMID: 36738159 DOI: 10.1111/mec.16873] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
The dynamic structure of ecological communities results from interactions among taxa that change with shifts in species composition in space and time. However, our ability to study the interplay of ecological and evolutionary processes on community assembly remains relatively unexplored due to the difficulty of measuring community structure over long temporal scales. Here, we made use of a geological chronosequence across the Hawaiian Islands, representing 50 years to 4.15 million years of ecosystem development, to sample 11 communities of arthropods and their associated plant taxa using semiquantitative DNA metabarcoding. We then examined how ecological communities changed with community age by calculating quantitative network statistics for bipartite networks of arthropod-plant associations. The average number of interactions per species (linkage density), ratio of plant to arthropod species (vulnerability) and uniformity of energy flow (interaction evenness) increased significantly in concert with community age. The index of specializationH 2 ' has a curvilinear relationship with community age. Our analyses suggest that younger communities are characterized by fewer but stronger interactions, while biotic associations become more even and diverse as communities mature. These shifts in structure became especially prominent on East Maui (~0.5 million years old) and older volcanos, after enough time had elapsed for adaptation and specialization to act on populations in situ. Such natural progression of specialization during community assembly is probably impeded by the rapid infiltration of non-native species, with special risk to younger or more recently disturbed communities that are composed of fewer specialized relationships.
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Affiliation(s)
- Natalie R Graham
- Department of Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Regional and Environmental Sciences, Trier University, Trier, Germany
| | - Jun Ying Lim
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Phillip Staniczenko
- Department of Biology, Brooklyn College, City University of New York, New York, New York, USA
| | - Jackson Callaghan
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, San Diego, California, USA
| | - Jeremy C Andersen
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Daniel S Gruner
- Department of Entomology, University of Maryland, College Park, Maryland, USA
| | - Rosemary G Gillespie
- Department of Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, California, USA
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9
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Borin JM, Lee JJ, Lucia-Sanz A, Gerbino KR, Weitz JS, Meyer JR. Rapid bacteria-phage coevolution drives the emergence of multiscale networks. Science 2023; 382:674-678. [PMID: 37943920 DOI: 10.1126/science.adi5536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023]
Abstract
Interactions between species catalyze the evolution of multiscale ecological networks, including both nested and modular elements that regulate the function of diverse communities. One common assumption is that such complex pattern formation requires spatial isolation or long evolutionary timescales. We show that multiscale network structure can evolve rapidly under simple ecological conditions without spatial structure. In just 21 days of laboratory coevolution, Escherichia coli and bacteriophage Φ21 coevolve and diversify to form elaborate cross-infection networks. By measuring ~10,000 phage-bacteria infections and testing the genetic basis of interactions, we identify the mechanisms that create each component of the multiscale pattern. Our results demonstrate how multiscale networks evolve in parasite-host systems, illustrating Darwin's idea that simple adaptive processes can generate entangled banks of ecological interactions.
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Affiliation(s)
- Joshua M Borin
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin J Lee
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adriana Lucia-Sanz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Krista R Gerbino
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua S Weitz
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institut de Biologie, École Normale Supérieure, 75005 Paris, France
| | - Justin R Meyer
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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10
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Gómez JM, González-Megías A, Armas C, Narbona E, Navarro L, Perfectti F. The role of phenotypic plasticity in shaping ecological networks. Ecol Lett 2023; 26 Suppl 1:S47-S61. [PMID: 37840020 DOI: 10.1111/ele.14192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 10/17/2023]
Abstract
Plasticity-mediated changes in interaction dynamics and structure may scale up and affect the ecological network in which the plastic species are embedded. Despite their potential relevance for understanding the effects of plasticity on ecological communities, these effects have seldom been analysed. We argue here that, by boosting the magnitude of intra-individual phenotypic variation, plasticity may have three possible direct effects on the interactions that the plastic species maintains with other species in the community: may expand the interaction niche, may cause a shift from one interaction niche to another or may even cause the colonization of a new niche. The combined action of these three factors can scale to the community level and eventually expresses itself as a modification in the topology and functionality of the entire ecological network. We propose that this causal pathway can be more widespread than previously thought and may explain how interaction niches evolve quickly in response to rapid changes in environmental conditions. The implication of this idea is not solely eco-evolutionary but may also help to understand how ecological interactions rewire and evolve in response to global change.
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Affiliation(s)
- José M Gómez
- Estación Experimental de Zonas Áridas (EEZA-CSIC), Almería, Spain
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | - Adela González-Megías
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Zoología, Universidad de Granada, Granada, Spain
| | - Cristina Armas
- Estación Experimental de Zonas Áridas (EEZA-CSIC), Almería, Spain
| | - Eduardo Narbona
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Luis Navarro
- Departamento de Biología Vegetal y Ciencias del Suelo, Universidad de Vigo, Vigo, Spain
| | - Francisco Perfectti
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Genética, Universidad de Granada, Granada, Spain
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11
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Zhu C, Li W, Campos-Arceiz A, Dalsgaard B, Ren P, Wang D, Zhang X, Sun M, Si Q, Kang Y, Ding P, Si X. The reliability of regional ecological knowledge to build local interaction networks: a test using seed-dispersal networks across land-bridge islands. Proc Biol Sci 2023; 290:20231221. [PMID: 37464753 PMCID: PMC10354482 DOI: 10.1098/rspb.2023.1221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/21/2023] [Indexed: 07/20/2023] Open
Abstract
Building ecological networks is the fundamental basis of depicting how species in communities interact, but sampling complex interaction networks is extremely labour intensive. Recently, indirect ecological information has been applied to build interaction networks. Here we propose to extend the source of indirect ecological information, and applied regional ecological knowledge to build local interaction networks. Using a high-resolution dataset consisting of 22 locally observed networks with 17 572 seed-dispersal events, we test the reliability of indirectly derived local networks based on regional ecological knowledge (REK) across islands. We found that species richness strongly influenced 'local interaction rewiring' (i.e. the proportion of locally observed interactions among regionally interacting species), and all network properties were biased using REK-based networks. Notably, species richness and local interaction rewiring strongly affected estimations of REK-based network structures. However, locally observed and REK-based networks detected the same trends of how network structure correlates to island area and isolation. These results suggest that we should use REK-based networks cautiously for reflecting actual interaction patterns of local networks, but highlight that REK-based networks have great potential for comparative studies across environmental gradients. The use of indirect regional ecological information may thus advance our understanding of biogeographical patterns of species interactions.
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Affiliation(s)
- Chen Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Wande Li
- Zhejiang Zhoushan Archipelago Observation and Research Station, Institute of Eco-Chongming, Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Ahimsa Campos-Arceiz
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan 666303, People's Republic of China
| | - Bo Dalsgaard
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Peng Ren
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Duorun Wang
- Zhejiang Zhoushan Archipelago Observation and Research Station, Institute of Eco-Chongming, Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Xue Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Minghao Sun
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Qi Si
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yi Kang
- Zhejiang Zhoushan Archipelago Observation and Research Station, Institute of Eco-Chongming, Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Ping Ding
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Xingfeng Si
- Zhejiang Zhoushan Archipelago Observation and Research Station, Institute of Eco-Chongming, Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, People's Republic of China
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12
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Xiang G, Jiang Y, Lan J, Huang L, Hao L, Liu Z, Xia J. Different influences of phylogenetically conserved and independent floral traits on plant functional specialization and pollination network structure. FRONTIERS IN PLANT SCIENCE 2023; 14:1084995. [PMID: 36760631 PMCID: PMC9902514 DOI: 10.3389/fpls.2023.1084995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Plant specialization and pollination network structure play important roles in community assembly. Floral traits can mediate plant-pollinator interactions and thus have important impacts on nestedness and modularity of pollination network. When such traits are phylogenetically conserved, therefore, phylogeny and traits should predict network structure to similar degrees. Moreover, conserved network structures were also found attributed to pollination syndrome or pollination system. However, we still know little about the relation between pollination syndrome and pollination network, especially under a phylogenetic framework. Herein, we established a phylogenetic framework including five floral traits (flower density, floral size, floral shape, floral symmetry, and floral color) and five species-level metrics (species strength, weighted closeness, specialization d', nestedness contribution, and modularity contribution) to test how floral traits could directly or indirectly influence species' specialization and network structure in central China. Phylogenetic signals were found in all floral traits except flower density. Structural equation model and phylogenetic structural equation model results showed that both floral size and floral density affected plant specialization and its contribution to network modularity indirectly. However, compared with phylogenetic independent flower density, phylogenetic conserved floral size had much more complexed influences, having a direct influence both on species' specialization and on modularity contribution. In this nested and modular network, abundant species with larger flowers tend to be more central and had larger values of z. Floral shape, symmetry, and color could act as co-flowering filters in pollination sharing and help to shape network modularity. Our results emphasize that phylogenetically conserved traits partially represent pollination syndrome and are important drivers for modular structure of local pollination network. This study may improve the understanding how the evolutionary history and ecological process drive local network structure and dynamics.
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Affiliation(s)
- Ganju Xiang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Yunyi Jiang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei, China
| | - Jinmao Lan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei, China
| | - Liuying Huang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei, China
| | - Lijun Hao
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei, China
| | - Zhiqian Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei, China
| | - Jing Xia
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, Hubei, China
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13
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McLeish MJ, Zamfir AD, Babalola BM, Peláez A, Fraile A, García-Arenal F. Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities. Virus Evol 2022; 8:veac095. [PMID: 36405340 PMCID: PMC9667876 DOI: 10.1093/ve/veac095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/24/2022] [Accepted: 09/30/2022] [Indexed: 07/22/2023] Open
Abstract
The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.
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Affiliation(s)
| | | | | | - Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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14
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Felix GM, Pinheiro RBP, Jorge LR, Lewinsohn TM. A framework for hierarchical compound topologies in species interaction networks. OIKOS 2022. [DOI: 10.1111/oik.09538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Gabriel M. Felix
- Univ. Estadual de Campinas, Depto de Biologia Animal, Inst. de Biologia Campinas Brazil
| | - Rafael B. P. Pinheiro
- Univ. Estadual de Campinas, Depto de Biologia Animal, Inst. de Biologia Campinas Brazil
| | - Leonardo R. Jorge
- Inst. of Entomology, Biology Centre of the Czech Academy of Sciences České Budějovice Czechia
| | - Thomas M. Lewinsohn
- Univ. Estadual de Campinas, Depto de Biologia Animal, Inst. de Biologia Campinas Brazil
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15
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Fricke EC, Hsieh C, Middleton O, Gorczynski D, Cappello CD, Sanisidro O, Rowan J, Svenning JC, Beaudrot L. Collapse of terrestrial mammal food webs since the Late Pleistocene. Science 2022; 377:1008-1011. [PMID: 36007038 DOI: 10.1126/science.abn4012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Food webs influence ecosystem diversity and functioning. Contemporary defaunation has reduced food web complexity, but simplification caused by past defaunation is difficult to reconstruct given the sparse paleorecord of predator-prey interactions. We identified changes to terrestrial mammal food webs globally over the past ~130,000 years using extinct and extant mammal traits, geographic ranges, observed predator-prey interactions, and deep learning models. Food webs underwent steep regional declines in complexity through loss of food web links after the arrival and expansion of human populations. We estimate that defaunation has caused a 53% decline in food web links globally. Although extinctions explain much of this effect, range losses for extant species degraded food webs to a similar extent, highlighting the potential for food web restoration via extant species recovery.
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Affiliation(s)
- Evan C Fricke
- Department of BioSciences, Rice University, Houston, TX, USA.,Department of Biology, University of Maryland, College Park, MD, USA.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chia Hsieh
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Owen Middleton
- School of Life Sciences, University of Sussex, Brighton, UK
| | | | | | - Oscar Sanisidro
- Departamento Ciencia de la Vida, Universidad de Alcalá, Alcalá de Henares, Spain
| | - John Rowan
- Department of Anthropology, University at Albany, Albany, NY, USA
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Lydia Beaudrot
- Department of BioSciences, Rice University, Houston, TX, USA
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16
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Pinheiro RBP, Felix GMF, Lewinsohn TM. Hierarchical compound topology uncovers complex structure of species interaction networks. J Anim Ecol 2022; 91:2248-2260. [DOI: 10.1111/1365-2656.13806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Rafael B. P. Pinheiro
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas Campinas SP Brazil
| | - Gabriel M. F. Felix
- Graduate Program in Ecology, Instituto de Biologia, Universidade Estadual de Campinas Campinas SP Brazil
| | - Thomas M. Lewinsohn
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas Campinas SP Brazil
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17
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Pereira J, Ribeiro MC, Battiston F, Jordán F. Reconstruction and variability of tropical pollination networks in the Brazilian Atlantic Forest. COMMUNITY ECOL 2022. [DOI: 10.1007/s42974-022-00106-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractLoss of biodiversity comprehends not only the extinction of individual species, but also the loss of the ecological interactions among them. Survival of species, continuation of ecosystem functioning in nature, and ecosystem services to humans depend on the maintenance of well-functioning networks of species interactions (e.g. plant–pollinator networks and food webs). Analyses of ecological networks often rely on biased and incomplete survey data, especially in species-rich areas, such as the tropics. We used a network inference method to reconstruct pollination data compiled from a large tropical rainforest habitat extent. To gain insight into the characteristics of plant–pollinator interactions across the region, we combined the reconstructed pollination network with species distribution modelling to obtain local pollination networks throughout the area. We explored how global network properties relate to natural forest cover and land cover heterogeneity. We found that some network properties (the sum and evenness of link weights, connectance and nestedness) are positively correlated with forest cover, indicating that networks in sites with more natural habitat have greater diversity of interactions. Modularity was not related to forest cover, but seemed to reflect habitat heterogeneity, due to the broad spatial scale of the study. We believe that the methodology suggested here can facilitate the use of incomplete network data in a reliable way and allow us to better understand and protect networks of species interactions in high biodiversity regions of the world.
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18
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DeSisto C, Herrera JP. Drivers and consequences of structure in plant-lemur ecological networks. J Anim Ecol 2022; 91:2010-2022. [PMID: 35837841 DOI: 10.1111/1365-2656.13776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Species interactions shape the diversity and resilience of ecological networks. Plant and animal traits, as well as phylogeny, affect interaction likelihood, driving variation in network structure and tolerance to disturbance. We investigated how traits and phylogenetic effects influenced network-wide interaction probabilities and examined the consequences of extinction on the structure and robustness of ecological networks. We combined both mutualistic and antagonistic interactions of animals (55 species, Infraorder Lemuriformes, Order Primates) and their food plants (590 genera) throughout Madagascar to generate ecological networks. We tested the effects of both lemur and plant traits, biogeographic factors, and phylogenetic relatedness on interaction probability in these networks using exponential random graph models. Next, we simulated animal and plant extinction to analyze the effects of extinction on network structure (connectance, nestedness, and modularity) and robustness for mutualistic, antagonistic, and combined plant-animal networks. Both animal and plant traits affected their interaction probabilities. Large, frugivorous lemurs with a short gestation length, occurring in arid habitats, and with a Least Concern threat level had a high interaction probability in the network, given all other variables. Closely related plants were more likely to interact with the same lemur species than distantly related plants, but closely related lemurs were not more likely to interact with the same plant genus. Simulated lemur extinction tended to increase connectance and modularity, but decrease nestedness and robustness, compared to pre-extinction networks. Networks were more tolerant to plant than lemur extinctions. Lemur-plant interactions were highly trait-structured and the loss of both lemurs and plants threatened the tolerance of mutualistic, antagonistic, and combined networks to future disturbance.
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Affiliation(s)
- Camille DeSisto
- Nicholas School of the Environment, Duke University, Durham, NC, USA
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19
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Affiliation(s)
- Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844
| | - Bob Week
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824
| | - Luke J. Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844
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20
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Darwell CT, Souto‐Vilarós D, Michalek J, Boutsi S, Isua B, Sisol M, Kuyaiva T, Weiblen G, Křivan V, Novotny V, Segar ST. Predicting distributions of
Wolbachia
strains through host ecological contact—Who's manipulating whom? Ecol Evol 2022; 12:e8826. [PMID: 35432921 PMCID: PMC9006231 DOI: 10.1002/ece3.8826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/23/2022] [Indexed: 12/05/2022] Open
Abstract
Reproductive isolation in response to divergent selection is often mediated via third‐party interactions. Under these conditions, speciation is inextricably linked to ecological context. We present a novel framework for understanding arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI). We predict that sympatric host sister‐species harbor paraphyletic Wolbachia strains that provide CI, while well‐defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia provides an adaptive advantage when coupled with reduced hybrid fitness, facilitating assortative mating between co‐occurring divergent phenotypes—the contact contingency hypothesis. To test this, we applied a predictive algorithm to empirical pollinating fig wasp data, achieving up to 91.60% accuracy. We further postulate that observed temporal decay of Wolbachia incidence results from adaptive host purging—adaptive decay hypothesis—but implementation failed to predict systematic patterns. We then account for post‐zygotic offspring mortality during CI mating, modeling fitness clines across developmental resources—the fecundity trade‐off hypothesis. This model regularly favored CI despite fecundity losses. We demonstrate that a rules‐based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely related sympatric species encounter adaptive disadvantage through hybridization.
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Affiliation(s)
- Clive T. Darwell
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency Khlong Luang Thailand
| | - Daniel Souto‐Vilarós
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
| | - Jan Michalek
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
| | - Sotiria Boutsi
- Agriculture & Environment Department Harper Adams University Newport UK
| | - Brus Isua
- The New Guinea Binatang Research Center Madang Papua New Guinea
| | - Mentap Sisol
- The New Guinea Binatang Research Center Madang Papua New Guinea
| | - Thomas Kuyaiva
- The New Guinea Binatang Research Center Madang Papua New Guinea
| | - George Weiblen
- Department of Plant & Microbial Biology Bell Museum University of Minnesota Saint Paul Minnesota USA
| | - Vlastimil Křivan
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
| | - Vojtech Novotny
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
| | - Simon T. Segar
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
- Agriculture & Environment Department Harper Adams University Newport UK
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21
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Pardo‐De la Hoz CJ, Medeiros ID, Gibert JP, Chagnon P, Magain N, Miadlikowska J, Lutzoni F. Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks. Ecol Evol 2022; 12:e8649. [PMID: 35261742 PMCID: PMC8888259 DOI: 10.1002/ece3.8649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/25/2021] [Accepted: 01/28/2022] [Indexed: 01/02/2023] Open
Abstract
Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss.
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Affiliation(s)
| | | | - Jean P. Gibert
- Department of BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Pierre‐Luc Chagnon
- Département des Sciences BiologiquesUniversité de MontréalMontréalQuébecCanada
| | - Nicolas Magain
- Biologie de l’évolution et de la ConservationUniversité de LiègeLiègeBelgium
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22
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Liu X, Shi Y, Yang T, Gao GF, Zhang L, Xu R, Li C, Liu R, Liu J, Chu H. Distinct Co-occurrence Relationships and Assembly Processes of Active Methane-Oxidizing Bacterial Communities Between Paddy and Natural Wetlands of Northeast China. Front Microbiol 2022; 13:809074. [PMID: 35154054 PMCID: PMC8826055 DOI: 10.3389/fmicb.2022.809074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/04/2022] [Indexed: 11/27/2022] Open
Abstract
Studies of methane-oxidizing bacteria are updating our views of their composition and function in paddy and natural wetlands. However, few studies have characterized differences in the methane-oxidizing bacterial communities between paddy and natural wetlands. Here, we conducted a 13C stable isotope-probing experiment and high-throughput sequencing to determine the structure profiling, co-occurrence relationships, and assembly processes of methanotrophic communities in four wetlands of Northeast China. There was a clear difference in community structure between paddy and natural wetlands. LEfSe analyses revealed that Methylobacter, FWs, and Methylosinus were enriched in natural wetlands, while Methylosarcina were prevailing in paddy, all identified as indicative methanotrophs. We observed distinct co-occurrence relationships between paddy and natural wetlands: more robust and complex connections in natural wetlands than paddy wetlands. Furthermore, the relative importance of stochastic processes was greater than that of deterministic processes, as stochastic processes explained >50% of the variation in communities. These results demonstrated that the co-occurrence relationships and assembly processes of active methanotrophic communities in paddy and natural wetlands were distinct. Overall, the results of this study enhance our understanding of the communities of methane-oxidizing bacteria in paddy and natural wetlands of Northeast China.
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Affiliation(s)
- Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liyan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Ruoyu Xu
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Chenxin Li
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Ruiyang Liu
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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23
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Puga-Caballero A, Lara C, Sánchez-González LA. From clustering to overdispersion: a north to south gradient in the patterns of phylogenetic structure in North American hummingbird assemblages. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00544-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Cuff JP, Windsor FM, Tercel MPTG, Kitson JJN, Evans DM. Overcoming the pitfalls of merging dietary metabarcoding into ecological networks. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jordan P. Cuff
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Fredric M. Windsor
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Maximillian P. T. G. Tercel
- School of Biosciences Cardiff University Cardiff UK
- Durrell Wildlife Conservation Trust Jersey Channel Islands
| | - James J. N. Kitson
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Darren M. Evans
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
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25
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Strydom T, Catchen MD, Banville F, Caron D, Dansereau G, Desjardins-Proulx P, Forero-Muñoz NR, Higino G, Mercier B, Gonzalez A, Gravel D, Pollock L, Poisot T. A roadmap towards predicting species interaction networks (across space and time). Philos Trans R Soc Lond B Biol Sci 2021; 376:20210063. [PMID: 34538135 PMCID: PMC8450634 DOI: 10.1098/rstb.2021.0063] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 11/12/2022] Open
Abstract
Networks of species interactions underpin numerous ecosystem processes, but comprehensively sampling these interactions is difficult. Interactions intrinsically vary across space and time, and given the number of species that compose ecological communities, it can be tough to distinguish between a true negative (where two species never interact) from a false negative (where two species have not been observed interacting even though they actually do). Assessing the likelihood of interactions between species is an imperative for several fields of ecology. This means that to predict interactions between species-and to describe the structure, variation, and change of the ecological networks they form-we need to rely on modelling tools. Here, we provide a proof-of-concept, where we show how a simple neural network model makes accurate predictions about species interactions given limited data. We then assess the challenges and opportunities associated with improving interaction predictions, and provide a conceptual roadmap forward towards predictive models of ecological networks that is explicitly spatial and temporal. We conclude with a brief primer on the relevant methods and tools needed to start building these models, which we hope will guide this research programme forward. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Tanya Strydom
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | - Michael D. Catchen
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Francis Banville
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- Université de Sherbrooke, Sherbrooke, Canada
| | - Dominique Caron
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Gabriel Dansereau
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | - Philippe Desjardins-Proulx
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | - Norma R. Forero-Muñoz
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | | | - Benjamin Mercier
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- Université de Sherbrooke, Sherbrooke, Canada
| | - Andrew Gonzalez
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Dominique Gravel
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- Université de Sherbrooke, Sherbrooke, Canada
| | - Laura Pollock
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Timothée Poisot
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
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26
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Moosmann M, Cuenca-Cambronero M, De Lisle S, Greenway R, Hudson CM, Lürig MD, Matthews B. On the evolution of trophic position. Ecol Lett 2021; 24:2549-2562. [PMID: 34553481 PMCID: PMC9290349 DOI: 10.1111/ele.13888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/24/2021] [Accepted: 08/26/2021] [Indexed: 01/05/2023]
Abstract
The trophic structure of food webs is primarily determined by the variation in trophic position among species and individuals. Temporal dynamics of food web structure are central to our understanding of energy and nutrient fluxes in changing environments, but little is known about how evolutionary processes shape trophic position variation in natural populations. We propose that trophic position, whose expression depends on both environmental and genetic determinants of the diet variation in individual consumers, is a quantitative trait that can evolve via natural selection. Such evolution can occur either when trophic position is correlated with other heritable morphological and behavioural traits under selection, or when trophic position is a target of selection, which is possible if the fitness effects of prey items are heterogeneously distributed along food chains. Recognising trophic position as an evolving trait, whose expression depends on the food web context, provides an important conceptual link between behavioural foraging theory and food web dynamics, and a useful starting point for the integration of ecological and evolutionary studies of trophic position.
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Affiliation(s)
- Marvin Moosmann
- Department of Fish Ecology and Evolution, EAWAG, Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Maria Cuenca-Cambronero
- Department of Fish Ecology and Evolution, EAWAG, Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Ryan Greenway
- Department of Fish Ecology and Evolution, EAWAG, Kastanienbaum, Switzerland
| | - Cameron M Hudson
- Department of Fish Ecology and Evolution, EAWAG, Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Blake Matthews
- Department of Fish Ecology and Evolution, EAWAG, Kastanienbaum, Switzerland
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27
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Maziarz M, Broughton RK, Casacci LP, Hebda G, Maák I, Trigos-Peral G, Witek M. Interspecific attraction between ground-nesting songbirds and ants: the role of nest-site selection. Front Zool 2021; 18:43. [PMID: 34507590 PMCID: PMC8434696 DOI: 10.1186/s12983-021-00429-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/30/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Interspecific interactions within ecological networks can influence animal fitness and behaviour, including nest-site selection of birds and ants. Previous studies revealed that nesting birds and ants may benefit from cohabitation, with interspecific attraction through their nest-site choice, but mutual interactions have not yet been tested. We explored a previously undescribed ecological link between ground-nesting birds and ants raising their own broods (larvae and pupae) within the birds' nests in a temperate primeval forest of lowland Europe. We tested whether the occurrence of ant broods within bird nests resulted from a mutual or one-sided interspecific attraction that operated through nest-site choice and was modified by weather conditions. RESULTS We found a non-random occupation of bird nests by ants raising their own broods within them, which indicated interspecific attraction driven solely by the ants. The birds' preference to nest near tussocks of vegetation showed little overlap with the most frequent placement of ant colonies among fallen deciduous tree-leaves, dead wood and moss. Additionally, birds did not appear to select forest localities with high densities of ant colonies. The occurrence of ant broods within bird nests was also unrelated to bird nest placement near to specific habitat features. The attractiveness of bird nests to ants appeared to increase with the thermal activity of the birds warming their nests, and also during cool and wet weather when the occurrence of ant broods within bird nests was most frequent. Ants often remained in the nests after the birds had vacated them, with only a slight reduction in the probability of ant brood occurrence over time. CONCLUSIONS The natural patterns of bird nest colonisation by ants support the hypothesis of ants' attraction to warm nests of birds to raise their broods under advantageous thermal conditions. Similar relationships may occur between other warm-blooded, nest-building vertebrates and nest-dwelling invertebrates, which depend on ambient temperatures. The findings advance our understanding of these poorly recognised interspecific interactions, and can inform future studies of ecological networks.
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Affiliation(s)
- Marta Maziarz
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.
| | - Richard K Broughton
- UK Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Luca Pietro Casacci
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
| | - Grzegorz Hebda
- Institute of Biology, University of Opole, Oleska 22, 45-052, Opole, Poland
| | - István Maák
- Department of Ecology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Gema Trigos-Peral
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Magdalena Witek
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
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Siwicka E, Gladstone‐Gallagher R, Hewitt JE, Thrush SF. Beyond the single index: Investigating ecological mechanisms underpinning ecosystem multifunctionality with network analysis. Ecol Evol 2021; 11:12401-12412. [PMID: 34594508 PMCID: PMC8462174 DOI: 10.1002/ece3.7987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Ecosystems simultaneously deliver multiple functions that relate to both the activities of resident species and environmental conditions. One of the biggest challenges in multifunctionality assessment is balancing analytical simplicity with ecosystem complexity. As an alternative to index-based approaches, we introduce a multivariate network analysis that uses network theory to assess multifunctionality in terms of the relationships between species' functional traits, environmental characteristics, and functions. We tested our approach in a complex and heterogeneous ecosystem, marine intertidal sandflats. We considered eight ecosystem function, five macrofaunal functional trait groups derived from 36 species, and four environmental characteristics. The indicators of ecosystem functions included the standing stock of primary producers, oxygen production, benthic oxygen consumption, DIN (ammonium and NOx efflux) and phosphate release from the sediments, denitrification, and organic matter degradation at the sediment surface. Trait clusters included functional groups of species that shared combinations of biological traits that affect ecosystem function: small mobile top 2 cm dwellers, suspension feeders, deep-dwelling worms, hard-bodied surface dwellers, and tube-forming worms. Environmental characteristics included sediment organic matter, %mud, %shell hash, and %sediment water content. Our results visualize and quantify how multiple ecosystem elements are connected and contribute to the provision of functions. Small mobile top 2 cm dwellers (among trait clusters) and %mud (among environmental characteristics) were the best predictor for multiple functions. Detailed knowledge of multifunctionality relationships can significantly increase our understanding of the real-world complexity of natural ecosystems. Multivariate network analysis, as a standalone method or applied alongside already existing single index multifunctionality methods, provides means to advance our understanding of how environmental change and biodiversity loss can influence ecosystem performance across multiple dimensions of functionality. Embedding such a detailed yet holistic multifunctionality assessment in environmental decision-making will support the assessment of multiple ecosystem services and social-ecological values.
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Affiliation(s)
- Ewa Siwicka
- Institute of Marine ScienceUniversity of AucklandAucklandNew Zealand
| | - Rebecca Gladstone‐Gallagher
- Institute of Marine ScienceUniversity of AucklandAucklandNew Zealand
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
| | - Judi E. Hewitt
- National Institute of Water and Atmospheric Research (NIWA)HamiltonNew Zealand
- Department of StatisticsUniversity of AucklandAucklandNew Zealand
| | - Simon F. Thrush
- Institute of Marine ScienceUniversity of AucklandAucklandNew Zealand
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29
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Emary C, Evans D. Can a complex ecosystem survive the loss of a large fraction of its species? A random matrix theory of secondary extinction. OIKOS 2021. [DOI: 10.1111/oik.08286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Clive Emary
- School of Mathematics, Statistics and Physics, Newcastle Univ. Newcastle‐upon‐Tyne UK
| | - Darren Evans
- School of Natural and Environmental Sciences, Newcastle Univ. Newcastle‐upon‐Tyne UK
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30
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Wang R, Yang Y, Jing Y, Segar ST, Zhang Y, Wang G, Chen J, Liu QF, Chen S, Chen Y, Cruaud A, Ding YY, Dunn DW, Gao Q, Gilmartin PM, Jiang K, Kjellberg F, Li HQ, Li YY, Liu JQ, Liu M, Machado CA, Ming R, Rasplus JY, Tong X, Wen P, Yang HM, Yang JJ, Yin Y, Zhang XT, Zhang YY, Yu H, Yue Z, Compton SG, Chen XY. Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association. Nat Ecol Evol 2021; 5:974-986. [PMID: 34002050 DOI: 10.1038/s41559-021-01469-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Many insects metamorphose from antagonistic larvae into mutualistic adult pollinators, with reciprocal adaptation leading to specialized insect-plant associations. It remains unknown how such interactions are established at molecular level. Here we assemble high-quality genomes of a fig species, Ficus pumila var. pumila, and its specific pollinating wasp, Wiebesia pumilae. We combine multi-omics with validation experiments to reveal molecular mechanisms underlying this specialized interaction. In the plant, we identify the specific compound attracting pollinators and validate the function of several key genes regulating its biosynthesis. In the pollinator, we find a highly reduced number of odorant-binding protein genes and an odorant-binding protein mainly binding the attractant. During antagonistic interaction, we find similar chemical profiles and turnovers throughout the development of galled ovules and seeds, and a significant contraction of detoxification-related gene families in the pollinator. Our study identifies some key genes bridging coevolved mutualists, establishing expectations for more diffuse insect-pollinator systems.
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Affiliation(s)
- Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Yang Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yi Jing
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, UK
| | - Yu Zhang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Gang Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jin Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | | | - Shan Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | | | - Yuan-Yuan Ding
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Derek W Dunn
- College of Life Sciences, Northwest University, Xi'an, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Philip M Gilmartin
- Department of Biological and Marine Science, University of Hull, Hull, UK
| | - Kai Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Finn Kjellberg
- CEFE, CNRS, University of Montpellier, Paul Valéry University Montpellier, EPHE, IRD, Montpellier, France
| | - Hong-Qing Li
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuan-Yuan Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Jian-Quan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Min Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Xin Tong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ping Wen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | | | - Jing-Jun Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xing-Tan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,School of Life Sciences, Qufu Normal University, Qufu, China.
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.
| | | | - Xiao-Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China. .,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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31
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Basset Y, Jorge LR, Butterill PT, Lamarre GPA, Dahl C, Ctvrtecka R, Gripenberg S, Lewis OT, Barrios H, Brown JW, Bunyavejchewin S, Butcher BA, Cognato AI, Davies SJ, Kaman O, Klimes P, Knížek M, Miller SE, Morse GE, Novotny V, Pongpattananurak N, Pramual P, Quicke DLJ, Sakchoowong W, Umari R, Vesterinen EJ, Weiblen G, Wright SJ, Segar ST. Host specificity and interaction networks of insects feeding on seeds and fruits in tropical rainforests. OIKOS 2021. [DOI: 10.1111/oik.08152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yves Basset
- ForestGEO, Smithsonian Tropical Research Inst., Apartado Balboa Ancon Panamá
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
- Maestria de Entomologia, Univ. de Panamá Panama City Republic of Panama
| | - Leonardo R. Jorge
- Faculty of Science, Univ. of South Bohemia Ceske Budejovice Czech Republic
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | - Philip T. Butterill
- Faculty of Science, Univ. of South Bohemia Ceske Budejovice Czech Republic
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | - Greg P. A. Lamarre
- ForestGEO, Smithsonian Tropical Research Inst., Apartado Balboa Ancon Panamá
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | - Chris Dahl
- Faculty of Science, Univ. of South Bohemia Ceske Budejovice Czech Republic
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | - Richard Ctvrtecka
- Faculty of Science, Univ. of South Bohemia Ceske Budejovice Czech Republic
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | - Sofia Gripenberg
- School of Biological Sciences, Univ. of Reading Reading Berkshire UK
| | | | - Héctor Barrios
- Maestria de Entomologia, Univ. de Panamá Panama City Republic of Panama
| | - John W. Brown
- National Museum of Natural History, Smithsonian Inst. Washington DC USA
| | | | - Buntika A. Butcher
- Dept of Biology, Faculty of Science, Integrative Ecology Laboratory, Chulalongkorn Univ. Phayathai Road Pathumwan Bangkok Thailand
- Center of Excellence in Entomology: Bee Biology, Diversity of Insects and Mites, Chulalongkorn Univ. Pathumwan Bangkok Thailand
| | - Anthony I. Cognato
- Dept of Entomology, Michigan State Univ., Natural Science Bldg. East Lansing MI USA
| | - Stuart J. Davies
- Forest Global Earth Observatory, Smithsonian Tropical Research Inst. and National Museum of Natural History Washington USA
| | - Ondrej Kaman
- Faculty of Science, Univ. of South Bohemia Ceske Budejovice Czech Republic
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | - Petr Klimes
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | - Miloš Knížek
- Forestry and Game Management Research Inst. Strnady Jíloviště Czech Republic
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Inst. Washington DC USA
| | | | - Vojtech Novotny
- Faculty of Science, Univ. of South Bohemia Ceske Budejovice Czech Republic
- Biology Centre of the Czech Academy of Sciences, Inst. of Entomology Ceske Budejovice Czech Republic
| | | | - Pairot Pramual
- Dept of Biology, Faculty of Science, Mahasarakham Univ., Kantharawichai District Maha Sarakham Thailand
| | - Donald L. J. Quicke
- Dept of Biology, Faculty of Science, Integrative Ecology Laboratory, Chulalongkorn Univ. Phayathai Road Pathumwan Bangkok Thailand
| | - Watana Sakchoowong
- Dept of National Parks, Forest Entomology Group, Wildlife and Plant Conservation Praholyothin Road Chatujak Bangkok Thailand
| | - Ruma Umari
- New Guinea Binatang Center Madang Papua New Guinea
| | - Eero J. Vesterinen
- Dept of Biology and Biodiversity Unit, Univ. of Turku Turku Finland
- Dept of Ecology, Swedish Univ. of Agricultural Sciences Uppsala Sweden
| | - George Weiblen
- Bell Museum and Dept of Plant and Microbial Biology, Univ. of Minnesota, Gortner Avenue St. Paul MN USA
| | - S. Joseph Wright
- ForestGEO, Smithsonian Tropical Research Inst. Balboa Ancon Panamá
| | - Simon T. Segar
- Agriculture and Environment Dept, Harper Adams Univ. Newport Shropshire UK
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32
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Yakovis E, Artemieva A. Effects of a trophic cascade on a multi-level facilitation cascade. J Anim Ecol 2021; 90:2462-2470. [PMID: 34143499 DOI: 10.1111/1365-2656.13558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/15/2021] [Indexed: 11/26/2022]
Abstract
The role of cascades in natural communities has been extensively studied, but interactions between trophic and facilitation cascades are unexplored. In the White Sea (65°N) shallow subtidal, bivalve primary facilitators provide hard substrate for secondary facilitator barnacles, that, in turn, provide substrate for conspecifics, ascidians, red algae and multiple associated organisms, composing a multi-level facilitation cascade. Previous research revealed that predation by the whelk Boreotrophon clathratus accounts for ~7% of adult barnacle mortality. Low whelk abundance limits their effect, with barnacles living on conspecifics several times more vulnerable to predation than those living on primary substrate. Trophic cascades can selectively shield foundation species from consumers, and hence may affect the structure and length of facilitation cascades. We tested the hypothesis that low abundance of the whelks results from mesopredator predation on their juveniles. Depending on the magnitude of the effect, this would mean that a trophic cascade controls the abundance of barnacles on all substrates or only barnacles living on conspecifics. We also suggested that barnacles on primary substrates and conspecifics facilitate different dependent assemblages. We manipulated the presence of crab and shrimp mesopredators in field caging experiments to assess their effect on whelk recruitment. In a field survey, we compared the assemblages of sessile macrobenthic organisms associated with barnacles living on different substrates. Caging experiments evidenced that crab and shrimp mesopredators reduce whelk recruitment by 4.6 times. Field data showed that barnacles on primary substrate and on conspecifics promote different dependent assemblages including secondary facilitator ascidians. Although mesopredators do not shield barnacles from elimination, their absence would restrict them from living on conspecifics. Barnacles on conspecifics are functionally different from barnacles on primary substrate, and can be considered a separate level of the facilitation cascade. Trophic cascades thus can generate community-wide effects on facilitation cascades by affecting their structure and possibly length.
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Affiliation(s)
- Eugeniy Yakovis
- Invertebrate Zoology Department, St.-Petersburg State University, Petersburg, Russia
| | - Anna Artemieva
- Invertebrate Zoology Department, St.-Petersburg State University, Petersburg, Russia
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33
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Fortin MJ, Dale MRT, Brimacombe C. Network ecology in dynamic landscapes. Proc Biol Sci 2021; 288:20201889. [PMID: 33906397 PMCID: PMC8080002 DOI: 10.1098/rspb.2020.1889] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/01/2021] [Indexed: 12/25/2022] Open
Abstract
Network ecology is an emerging field that allows researchers to conceptualize and analyse ecological networks and their dynamics. Here, we focus on the dynamics of ecological networks in response to environmental changes. Specifically, we formalize how network topologies constrain the dynamics of ecological systems into a unifying framework in network ecology that we refer to as the 'ecological network dynamics framework'. This framework stresses that the interplay between species interaction networks and the spatial layout of habitat patches is key to identifying which network properties (number and weights of nodes and links) and trade-offs among them are needed to maintain species interactions in dynamic landscapes. We conclude that to be functional, ecological networks should be scaled according to species dispersal abilities in response to landscape heterogeneity. Determining how such effective ecological networks change through space and time can help reveal their complex dynamics in a changing world.
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Affiliation(s)
- Marie-Josée Fortin
- Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Mark R. T. Dale
- Ecosystem Science and Management, University of Northern British Columbia, Prince George, British Columbia, Canada
| | - Chris Brimacombe
- Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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34
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Deng X, Chen L, Tian E, Zhang D, Wattana T, Yu H, Kjellberg F, Segar ST. Low host specificity and broad geographical ranges in a community of parasitic non-pollinating fig wasps (Sycoryctinae; Chalcidoidea). J Anim Ecol 2021; 90:1678-1690. [PMID: 33738802 DOI: 10.1111/1365-2656.13483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 02/26/2021] [Indexed: 12/23/2022]
Abstract
Plants, phytophagous insects and their parasitoids form the most diverse assemblages of macroscopic organisms on earth. Enclosed assemblages in particular represent a tractable system for studying community assembly and diversification. Communities associated with widespread plant species are especially suitable as they facilitate a comparative approach. Pantropical fig-wasp communities represent a remarkably well-replicated system, ideal for studying these historical processes. We expect high dispersal ability in non-pollinating fig wasps to result in lower geographical turnover in comparison to pollinating fig wasps. The ability of non-pollinating wasps to utilise a number of hosts (low host specificity) is a key determinant of overall geographical range, with intraspecific competition becoming a constraining factor should diet breadth overlap among species. Finally, we expect conserved community structure throughout the host range. We aim to test these expectations, derived from population genetic and community studies, using the multi-trophic insect community associated with Ficus hirta throughout its 3,500 km range across continental and insular Asia. We collect molecular evidence from one coding mitochondrial gene, one non-coding nuclear gene and multiple microsatellites across 25 geographical sites. Using these data, we establish species boundaries, determine levels of host specificity among non-pollinating fig wasps and quantify geographical variation in community composition. We find low host specificity in two genera of non-pollinating fig wasps. Functional community structure is largely conserved across the range of the host fig, despite limited correspondence between the ranges of non-pollinator and pollinator species. While nine pollinators are associated with Ficus hirta, the two non-pollinator tribes developing in its figs each contained only four species. Contrary to predictions, we find stronger isolation by distance in non-pollinators than pollinators. Long-lived non-pollinators may disperse more gradually and be less reliant on infrequent long-distance dispersal by wind currents. Segregation among non-pollinating species across their range is suggestive of competitive exclusion and we propose that this may be a result of increased levels of local adaptation and moderate, but regular, rates of dispersal. Our findings provide one more example of lack of strict codiversification in the geographical diversification of plant-associated insect communities.
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Affiliation(s)
- Xiaoxia Deng
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China.,Centre for Plant Ecology, CAS Core Botanical Gardens, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Lianfu Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China.,Centre for Plant Ecology, CAS Core Botanical Gardens, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Enwei Tian
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China
| | - Dayong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | | | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, CAS, Guangzhou, China.,Centre for Plant Ecology, CAS Core Botanical Gardens, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Finn Kjellberg
- CEFE, University of Montpellier, CNRS, University of Paul Valéry Montpellier, EPHE, IRD, Montpellier Cedex 5, France
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, UK
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35
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Naniwadekar R, Gopal A, Page N, Ghuman S, Ramachandran V, Joshi J. Large frugivores matter more on an island: Insights from island-mainland comparison of plant-frugivore communities. Ecol Evol 2021; 11:1399-1412. [PMID: 33598140 PMCID: PMC7863668 DOI: 10.1002/ece3.7151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/20/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Endozoochory, a mutualistic interaction between plants and frugivores, is one of the key processes responsible for maintenance of tropical biodiversity. Islands, which have a smaller subset of plants and frugivores when compared with mainland communities, offer an interesting setting to understand the organization of plant-frugivore communities vis-a-vis the mainland sites. We examined the relative influence of functional traits and phylogenetic relationships on the plant-seed disperser interactions on an island and a mainland site. The island site allowed us to investigate the organization of the plant-seed disperser community in the natural absence of key frugivore groups (bulbuls and barbets) of Asian tropics. The endemic Narcondam Hornbill was the most abundant frugivore on the island and played a central role in the community. Species strength of frugivores (a measure of relevance of frugivores for plants) was positively associated with their abundance. Among plants, figs had the highest species strength and played a central role in the community. Island-mainland comparison revealed that the island plant-seed disperser community was more asymmetric, connected, and nested as compared to the mainland community. Neither phylogenetic relationships nor functional traits (after controlling for phylogenetic relationships) were able to explain the patterns of interactions between plants and frugivores on the island or the mainland pointing toward the diffused nature of plant-frugivore interactions. The diffused nature is a likely consequence of plasticity in foraging behavior and trait convergence that contribute to governing the interactions between plants and frugivores. This is one of the few studies to compare the plant-seed disperser communities between a tropical island and mainland and demonstrates key role played by a point-endemic frugivore in seed dispersal on island.
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Affiliation(s)
| | | | | | | | - Vivek Ramachandran
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Jahnavi Joshi
- CSIR‐Centre for Cellular and Molecular BiologyHyderabadIndia
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36
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Guimarães PR. The Structure of Ecological Networks Across Levels of Organization. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-012220-120819] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challenge is to understand the amount of interdependence as we move from individual-based networks to species-based networks and beyond. Despite the uneven distribution of studies, regularities in network structure emerge across scales due to the fundamental architectural patterns shared by complex networks and the interplay between traits and numerical effects. I illustrate the integration of these organizational scales by exploring the consequences of the emergence of highly connected species for network structures across scales.
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Affiliation(s)
- Paulo R. Guimarães
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
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37
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Anderson J, Song BH. Plant adaptation to climate change - Where are we? JOURNAL OF SYSTEMATICS AND EVOLUTION 2020; 58:533-545. [PMID: 33584833 PMCID: PMC7875155 DOI: 10.1111/jse.12649] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Climate change poses critical challenges for population persistence in natural communities, agriculture and environmental sustainability, and food security. In this review, we discuss recent progress in climatic adaptation in plants. We evaluate whether climate change exerts novel selection and disrupts local adaptation, whether gene flow can facilitate adaptive responses to climate change, and if adaptive phenotypic plasticity could sustain populations in the short term. Furthermore, we discuss how climate change influences species interactions. Through a more in-depth understanding of these eco-evolutionary dynamics, we will increase our capacity to predict the adaptive potential of plants under climate change. In addition, we review studies that dissect the genetic basis of plant adaptation to climate change. Finally, we highlight key research gaps, ranging from validating gene function, to elucidating molecular mechanisms, expanding research systems from model species to other natural species, testing the fitness consequences of alleles in natural environments, and designing multifactorial studies that more closely reflect the complex and interactive effects of multiple climate change factors. By leveraging interdisciplinary tools (e.g., cutting-edge omics toolkits, novel ecological strategies, newly-developed genome editing technology), researchers can more accurately predict the probability that species can persist through this rapid and intense period of environmental change, as well as cultivate crops to withstand climate change, and conserve biodiversity in natural systems.
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Affiliation(s)
- Jill Anderson
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Authors for correspondence. Bao-Hua Song. ; Jill Anderson.
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Authors for correspondence. Bao-Hua Song. ; Jill Anderson.
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38
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On the Perils of Ignoring Evolution in Networks. Trends Ecol Evol 2020; 35:865-866. [PMID: 32854959 DOI: 10.1016/j.tree.2020.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/24/2022]
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Rossberg AG. What Are the Fundamental Questions Regarding Evolution in Ecological Networks? Trends Ecol Evol 2020; 35:863-865. [PMID: 32674868 DOI: 10.1016/j.tree.2020.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Axel G Rossberg
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
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Sagoff M. Ecological Networks: Response to Segar et al. Trends Ecol Evol 2020; 35:862-863. [PMID: 32408997 DOI: 10.1016/j.tree.2020.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 11/17/2022]
Affiliation(s)
- Mark Sagoff
- Institute for Philosophy and Public Policy, George Mason University, Fairfax, VA, USA.
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Mutual Information as a General Measure of Structure in Interaction Networks. ENTROPY 2020; 22:e22050528. [PMID: 33286300 PMCID: PMC7517023 DOI: 10.3390/e22050528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022]
Abstract
Entropy-based indices are long-established measures of biological diversity, nowadays used to gauge partitioning of diversity at different spatial scales. Here, we tackle the measurement of diversity of interactions among two sets of organisms, such as plants and their pollinators. Actual interactions in ecological communities are depicted as bipartite networks or interaction matrices. Recent studies concentrate on distinctive structural patterns, such as nestedness or modularity, found in different modes of interaction. By contrast, we investigate mutual information as a general measure of structure in interactive networks. Mutual information (MI) measures the degree of reciprocal matching or specialization between interacting organisms. To ascertain its usefulness as a general measure, we explore (a) analytical solutions for different models; (b) the response of MI to network parameters, especially size and occupancy; (c) MI in nested, modular, and compound topologies. MI varies with fundamental matrix parameters: dimension and occupancy, for which it can be adjusted or normalized. Apparent differences among topologies are contingent on dimensions and occupancy, rather than on topological patterns themselves. As a general measure of interaction structure, MI is applicable to conceptually and empirically fruitful analyses, such as comparing similar ecological networks along geographical gradients or among interaction modalities in mutualistic or antagonistic networks.
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Richardson BJ. Evolutionary biogeography of Australian jumping spider genera (Araneae : Salticidae). AUST J ZOOL 2019. [DOI: 10.1071/zo20023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phylogenetic relationships and estimated dates of origin, plus distributional, ecological and morphological data for salticid genera were used to examine a series of hypotheses related to the evolution of the Australian salticid fauna. Though independent, the time patterns of evolution of genera in Australia and South America were similar, while that for Northern Hemisphere taxa differed. In each case the production of new genera occurred during the warmer parts of the mid Tertiary but not during cooler and drier times. Asian elements entered Australia as early as 31 million years ago, long before the collision of the Australasian and Asian continental plates. Endemic and derivatives of Asian genera were similarly distributed across Australian biomes. However, arriving taxa were more successful when conditions matched their mesic origins (tropical), but less so when different (temperate). While endemic genera often extended their ranges into drier environments by increasing the number of species, recent arrivals did so by extending the range of individual species. Maximum Parsimony analyses of a range of presumed adaptive, morphological and ecological characters showed these did not reflect genus-level processes; however, the analysis did show all endemic genera had mesic origins.
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