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Salim JA, Saraiva AM, Zermoglio PF, Agostini K, Wolowski M, Drucker DP, Soares FM, Bergamo PJ, Varassin IG, Freitas L, Maués MM, Rech AR, Veiga AK, Acosta AL, Araujo AC, Nogueira A, Blochtein B, Freitas BM, Albertini BC, Maia-Silva C, Nunes CEP, Pires CSS, dos Santos CF, Queiroz EP, Cartolano EA, de Oliveira FF, Amorim FW, Fontúrbel FE, da Silva GV, Consolaro H, Alves-dos-Santos I, Machado IC, Silva JS, Aleixo KP, Carvalheiro LG, Rocca MA, Pinheiro M, Hrncir M, Streher NS, Ferreira PA, de Albuquerque PMC, Maruyama PK, Borges RC, Giannini TC, Brito VLG. Data standardization of plant-pollinator interactions. Gigascience 2022; 11:giac043. [PMID: 35639882 PMCID: PMC9154084 DOI: 10.1093/gigascience/giac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing. RESULTS Here we present a vocabulary of terms and a data model for sharing plant-pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant-pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant-pollinator interactions. CONCLUSIONS The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant-pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant-pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of terms.
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Affiliation(s)
- José A Salim
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Antonio M Saraiva
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Paula F Zermoglio
- Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Kayna Agostini
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Rodovia Anhanguera km 174, Araras, São Paulo, Caixa Postal 153. CEP 13600-970, Brazil
| | - Marina Wolowski
- Instituto de Ciências da Natureza, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva 700, Alfenas, Minas Gerais, 37130-001, Brazil
| | - Debora P Drucker
- Embrapa Agricultura Digital, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, SP, Brazil
| | - Filipi M Soares
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Pedro J Bergamo
- Jardim Botânico do Rio de Janeiro, R. Pacheco Leão 915, Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - Isabela G Varassin
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Leandro Freitas
- Jardim Botânico do Rio de Janeiro, R. Pacheco Leão 915, Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - Márcia M Maués
- Laboratório de Entomologia, Embrapa Amazônia Oriental, Trav. Dr. Enéas Pinheiro, s/n°, Bairro do Marco, Belém, Pará, 66095-903, Brazil
| | - Andre R Rech
- Faculdade Interdisciplinar de Humanidades, Centro Multiusuário de Pesquisa em Ciência Florestal (MULTIFLOR), Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, 39100-000, Brazil
| | - Allan K Veiga
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Andre L Acosta
- Instituto Tecnológico Vale. Rua Boaventura da Silva, 955, 66055-900, Belém, Pará, Brazil
| | - Andréa C Araujo
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Anselmo Nogueira
- Laboratório de Interações Plant-Animal (LIPA), Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC, Alameda da Universidade, s/nº, Anchieta, São Bernardo do Campo, São Paulo, Brazil
| | - Betina Blochtein
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 90619-900, Brazil
| | - Breno M Freitas
- Departamento de Zootecnia, Campus Universitário do Pici, Universidade Federal do Ceará, Centro de Ciências Agrárias, Fortaleza, CE, Brazil
| | - Bruno C Albertini
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Camila Maia-Silva
- Departamento de Biociências, Universidade Federal Rural do Semi-Árido, Av. Francisco Mota, n° 572, Presidente Costa e Silva, Mossoró, RN, 59625-900, Brazil
| | - Carlos E P Nunes
- Department of Biological and Environmental Sciences, Cottrell Building, University of Stirling, Stirling FK9 4LA, Scotland, United Kingdom
| | - Carmen S S Pires
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
| | - Charles F dos Santos
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 90619-900, Brazil
| | - Elisa P Queiroz
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Etienne A Cartolano
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Favízia F de Oliveira
- Laboratório de Bionomia, Biogeografia e Sistemática de Insetos (BIOSIS), Instituto de Biologia (IBIO), Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Felipe W Amorim
- Laboratório de Ecologia da Polinização e Interações (LEPI), Programa de Pós-graduação em Botânica, Programa de Pós-graduação em Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Francisco E Fontúrbel
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Gleycon V da Silva
- Programa de Pós-Graduação em Ecologia / INPA-V8 - Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, 69067-375, Manaus - AM, Brazil
| | - Hélder Consolaro
- Instituto de Biotecnologia, Universidade Federal de Catalão, Catalão, Goiás, Brazil
| | - Isabel Alves-dos-Santos
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Isabel C Machado
- Programa de Pós-Graduação em Biologia Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil
| | - Juliana S Silva
- Instituto Federal de Educação Ciência e Tecnologia de Mato Grosso, Avenida Sen. Filinto Müller, 953 - CEP: 78043-400 - Cuiabá, MT, Brazil
| | - Kátia P Aleixo
- Associação Brasileira de Estudos das Abelhas (A.B.E.L.H.A.), São Paulo, SP, 04535-001, Brazil
| | - Luísa G Carvalheiro
- Departamento de Ecologia, Universidade Federal de Goiás, Campus Samambaia, Goiânia, Brazil Centre for Ecology, Evolution and Environmental Changes (cE3c), University of Lisboa, Lisbon, Portugal
| | - Márcia A Rocca
- Departamento de Ecologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Sergipe, Avenida Marechal Rondon s/n, São Cristóvão, Sergipe, 49100-000, Brazil
| | - Mardiore Pinheiro
- Universidade Federal da Fronteira Sul, R. Major Antônio Cardoso 590, Cerro Largo, Rio Grande do Sul, 97900-000, Brazil
| | - Michael Hrncir
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 321, Travessa 14, São Paulo, São Paulo, 05508-900, Brazil
| | - Nathália S Streher
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA,15260, United States of America
| | - Patricia A Ferreira
- Environmental Sciences Department, Federal University of São Carlos, São Paulo, Brazil
| | | | - Pietro K Maruyama
- Centro de Síntese Ecológica e Conservação, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafael C Borges
- Instituto Tecnológico Vale. Rua Boaventura da Silva, 955, 66055-900, Belém, Pará, Brazil
| | - Tereza C Giannini
- Instituto Tecnológico Vale. Rua Boaventura da Silva, 955, 66055-900, Belém, Pará, Brazil
| | - Vinícius L G Brito
- Instituto de Biologia, Universidade Federal de Uberlândia, Rua Ceará sn, Uberlândia, Minas Gerais, 38.405-302, Brazil
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Morton DN, Lafferty KD. Parasites in kelp‐forest food webs increase food‐chain length, complexity, and specialization, but reduce connectance. ECOL MONOGR 2022; 92:e1506. [PMID: 35865510 PMCID: PMC9286845 DOI: 10.1002/ecm.1506] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/15/2021] [Accepted: 10/26/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Dana N. Morton
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara California USA
- Marine Science Institute University of California Santa Barbara California USA
| | - Kevin D. Lafferty
- U.S. Geological Survey, Western Ecological Research Center, at Marine Science Institute University of California Santa Barbara California USA
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Del Risco AA, Montoya ÁM, García V, Currea S, Rivera YA, Moreno D, Rodríguez ÁT. Data synthesis and dynamic visualization converge into a comprehensive biotic interaction network: a case study of the urban and rural areas of Bogotá D.C. Urban Ecosyst 2021. [DOI: 10.1007/s11252-021-01133-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Schlenger AJ, Beas-Luna R, Ambrose RF. Forecasting ocean acidification impacts on kelp forest ecosystems. PLoS One 2021; 16:e0236218. [PMID: 33886569 PMCID: PMC8061940 DOI: 10.1371/journal.pone.0236218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 03/28/2021] [Indexed: 11/19/2022] Open
Abstract
Ocean acidification is one the biggest threats to marine ecosystems worldwide, but its ecosystem wide responses are still poorly understood. This study integrates field and experimental data into a mass balance food web model of a temperate coastal ecosystem to determine the impacts of specific OA forcing mechanisms as well as how they interact with one another. Specifically, we forced a food web model of a kelp forest ecosystem near its southern distribution limit in the California large marine ecosystem to a 0.5 pH drop over the course of 50 years. This study utilizes a modeling approach to determine the impacts of specific OA forcing mechanisms as well as how they interact. Isolating OA impacts on growth (Production), mortality (Other Mortality), and predation interactions (Vulnerability) or combining all three mechanisms together leads to a variety of ecosystem responses, with some taxa increasing in abundance and other decreasing. Results suggest that carbonate mineralizing groups such as coralline algae, abalone, snails, and lobsters display the largest decreases in biomass while macroalgae, urchins, and some larger fish species display the largest increases. Low trophic level groups such as giant kelp and brown algae increase in biomass by 16% and 71%, respectively. Due to the diverse way in which OA stress manifests at both individual and population levels, ecosystem-level effects can vary and display nonlinear patterns. Combined OA forcing leads to initial increases in ecosystem and commercial biomasses followed by a decrease in commercial biomass below initial values over time, while ecosystem biomass remains high. Both biodiversity and average trophic level decrease over time. These projections indicate that the kelp forest community would maintain high productivity with a 0.5 drop in pH, but with a substantially different community structure characterized by lower biodiversity and relatively greater dominance by lower trophic level organisms.
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Affiliation(s)
- Adam J. Schlenger
- Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, California, United States of America
| | - Rodrigo Beas-Luna
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada B.C. Mexico
| | - Richard F. Ambrose
- Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Environmental Health Sciences, University of California, Los Angeles, Los Angeles, California, United States of America
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5
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Morton DN, Antonino CY, Broughton FJ, Dykman LN, Kuris AM, Lafferty KD. A food web including parasites for kelp forests of the Santa Barbara Channel, California. Sci Data 2021; 8:99. [PMID: 33833244 PMCID: PMC8032823 DOI: 10.1038/s41597-021-00880-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/19/2021] [Indexed: 11/28/2022] Open
Abstract
We built a high-resolution topological food web for the kelp forests of the Santa Barbara Channel, California, USA that includes parasites and significantly improves resolution compared to previous webs. The 1,098 nodes and 21,956 links in the web describe an economically, socially, and ecologically vital system. Nodes are broken into life-stages, with 549 free-living life-stages (492 species from 21 Phyla) and 549 parasitic life-stages (450 species from 10 Phyla). Links represent three kinds of trophic interactions, with 9,352 predator-prey links, 2,733 parasite-host links and 9,871 predator-parasite links. All decisions for including nodes and links are documented, and extensive metadata in the node list allows users to filter the node list to suit their research questions. The kelp-forest food web is more species-rich than any other published food web with parasites, and it has the largest proportion of parasites. Our food web may be used to predict how kelp forests may respond to change, will advance our understanding of parasites in ecosystems, and fosters development of theory that incorporates large networks.
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Affiliation(s)
- Dana N Morton
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106-6150, USA.
- Marine Science Institute, University of California, Santa Barbara, CA, 93106-9610, USA.
| | - Cristiana Y Antonino
- College of Creative Studies, University of California, Santa Barbara, CA, 93106-6150, USA
| | - Farallon J Broughton
- College of Creative Studies, University of California, Santa Barbara, CA, 93106-6150, USA
| | - Lauren N Dykman
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106-6150, USA
| | - Armand M Kuris
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106-6150, USA
- Marine Science Institute, University of California, Santa Barbara, CA, 93106-9610, USA
| | - Kevin D Lafferty
- Western Ecological Research Center, U.S. Geological Survey, at Marine Science Institute, University of California, Santa Barbara, CA, 93106-9610, USA
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Beas-Luna R, Micheli F, Woodson CB, Carr M, Malone D, Torre J, Boch C, Caselle JE, Edwards M, Freiwald J, Hamilton SL, Hernandez A, Konar B, Kroeker KJ, Lorda J, Montaño-Moctezuma G, Torres-Moye G. Geographic variation in responses of kelp forest communities of the California Current to recent climatic changes. GLOBAL CHANGE BIOLOGY 2020; 26:6457-6473. [PMID: 32902090 DOI: 10.1111/gcb.15273] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/06/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
The changing global climate is having profound effects on coastal marine ecosystems around the world. Structure, functioning, and resilience, however, can vary geographically, depending on species composition, local oceanographic forcing, and other pressures from human activities and use. Understanding ecological responses to environmental change and predicting changes in the structure and functioning of whole ecosystems require large-scale, long-term studies, yet most studies trade spatial extent for temporal duration. We address this shortfall by integrating multiple long-term kelp forest monitoring datasets to evaluate biogeographic patterns and rates of change of key functional groups (FG) along the west coast of North America. Analysis of data from 469 sites spanning Alaska, USA, to Baja California, Mexico, and 373 species (assigned to 18 FG) reveals regional variation in responses to both long-term (2006-2016) change and a recent marine heatwave (2014-2016) associated with two atmospheric and oceanographic anomalies, the "Blob" and extreme El Niño Southern Oscillation (ENSO). Canopy-forming kelps appeared most sensitive to warming throughout their range. Other FGs varied in their responses among trophic levels, ecoregions, and in their sensitivity to heatwaves. Changes in community structure were most evident within the southern and northern California ecoregions, while communities in the center of the range were more resilient. We report a poleward shift in abundance of some key FGs. These results reveal major, ongoing region-wide changes in productive coastal marine ecosystems in response to large-scale climate variability, and the potential loss of foundation species. In particular, our results suggest that coastal communities that are dependent on kelp forests will be more impacted in the southern portion of the California Current region, highlighting the urgency of implementing adaptive strategies to sustain livelihoods and ensure food security. The results also highlight the value of multiregional integration and coordination of monitoring programs for improving our understanding of marine ecosystems, with the goal of informing policy and resource management in the future.
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Affiliation(s)
| | - Fiorenza Micheli
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
- Stanford Center for Ocean Solutions, Stanford University, Pacific Grove, CA, USA
| | - C Brock Woodson
- College of Engineering, University of Georgia, Athens, GA, USA
| | - Mark Carr
- University of California, Santa Cruz, CA, USA
| | - Dan Malone
- University of California, Santa Cruz, CA, USA
| | - Jorge Torre
- Comunidad y Biodiversidad A.C., La Paz, Mexico
| | - Charles Boch
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Southwest Fisheries Science Center, NOAA, San Diego, CA, USA
| | - Jennifer E Caselle
- Marine Science Institute, University of California, Santa Barbara, CA, USA
| | | | - Jan Freiwald
- University of California, Santa Cruz, CA, USA
- Reef Check California, Marina del Rey, CA, USA
| | - Scott L Hamilton
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, USA
| | | | | | | | - Julio Lorda
- Universidad Autónoma de Baja California, Ensenada, Mexico
- Tijuana River National Estuarine Research Reserve, Imperial Beach, CA, USA
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Ollivier M, Lesieur V, Raghu S, Martin JF. Characterizing ecological interaction networks to support risk assessment in classical biological control of weeds. CURRENT OPINION IN INSECT SCIENCE 2020; 38:40-47. [PMID: 32088650 DOI: 10.1016/j.cois.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/04/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
A key element in weed biological control is the selection of a biological control agent that minimizes the risks of non-target attack and indirect effects on the recipient community. Network ecology is a promising approach that could help decipher tritrophic interactions in both the native and the invaded ranges, to complement quarantine-based host-specificity tests and gain insights on potential interactions of biological control agents. This review highlights practical questions addressed by networks, including 1) biological control agent selection, based on specialization indices, 2) risk assessment of biological control agent release into a novel environment, via particular patterns of association such as apparent competition between agent(s) and native herbivore(s), 3) network comparisons through structural metrics, 4) potential of network modelling and 5) limits of network construction methods.
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Affiliation(s)
- Melodie Ollivier
- CBGP, Montpellier SupAgro, INRAE, CIRAD, IRD, Univ Montpellier, Montpellier, France.
| | - Vincent Lesieur
- CBGP, Montpellier SupAgro, INRAE, CIRAD, IRD, Univ Montpellier, Montpellier, France; CSIRO Health and Biosecurity, European Laboratory, Montferrier sur Lez, 34980, France
| | | | - Jean-François Martin
- CBGP, Montpellier SupAgro, INRAE, CIRAD, IRD, Univ Montpellier, Montpellier, France
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Low NHN, Micheli F. Short- and long-term impacts of variable hypoxia exposures on kelp forest sea urchins. Sci Rep 2020; 10:2632. [PMID: 32060309 PMCID: PMC7021826 DOI: 10.1038/s41598-020-59483-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 01/30/2020] [Indexed: 11/08/2022] Open
Abstract
Climate change is altering the intensity and variability of environmental stress that organisms and ecosystems experience, but effects of changing stress regimes are not well understood. We examined impacts of constant and variable sublethal hypoxia exposures on multiple biological processes in the sea urchin Strongylocentrotus purpuratus, a key grazer in California Current kelp forests, which experience high variability in physical conditions. We quantified metabolic rates, grazing, growth, calcification, spine regeneration, and gonad production under constant, 3-hour variable, and 6-hour variable exposures to sublethal hypoxia, and compared responses for each hypoxia regime to normoxic conditions. Sea urchins in constant hypoxia maintained baseline metabolic rates, but had lower grazing, gonad development, and calcification rates than those in ambient conditions. The sublethal impacts of variable hypoxia differed among biological processes. Spine regrowth was reduced under all hypoxia treatments, calcification rates under variable hypoxia were intermediate between normoxia and constant hypoxia, and gonad production correlated negatively with continuous time under hypoxia. Therefore, exposure variability can differentially modulate the impacts of sublethal hypoxia, and may impact sea urchin populations and ecosystems via reduced feeding and reproduction. Addressing realistic, multifaceted stressor exposures and multiple biological responses is crucial for understanding climate change impacts on species and ecosystems.
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Affiliation(s)
- Natalie H N Low
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, 93950, USA.
| | - Fiorenza Micheli
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, 93950, USA
- Stanford Center for Ocean Solutions, Pacific Grove, CA, 93950, USA
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9
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Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG. Bipartite graphs in systems biology and medicine: a survey of methods and applications. Gigascience 2018; 7:1-31. [PMID: 29648623 PMCID: PMC6333914 DOI: 10.1093/gigascience/giy014] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 01/15/2018] [Accepted: 02/13/2018] [Indexed: 11/14/2022] Open
Abstract
The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.
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Affiliation(s)
- Georgios A Pavlopoulos
- Lawrence Berkeley Labs, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Panagiota I Kontou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eylül University, 35340, Turkey
| | - Costas Bouyioukos
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, France
| | - Evripides Markou
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
| | - Pantelis G Bagos
- University of Thessaly, Department of Computer Science and Biomedical Informatics, Papasiopoulou 2–4, Lamia, 35100, Greece
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Lau MK, Borrett SR, Baiser B, Gotelli NJ, Ellison AM. Ecological network metrics: opportunities for synthesis. Ecosphere 2017. [DOI: 10.1002/ecs2.1900] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Matthew K. Lau
- Harvard Forest Harvard University Petersham Massachusetts 02138 USA
| | - Stuart R. Borrett
- Department of Biology and Marine Biology University of North Carolina Wilmington North Carolina 28403 USA
- Duke Network Analysis Center Social Science Research Institute Duke University Durham North Carolina 27708 USA
| | - Benjamin Baiser
- Department of Wildlife Ecology and Conservation University of Florida Gainesville Florida 32611 USA
| | | | - Aaron M. Ellison
- Harvard Forest Harvard University Petersham Massachusetts 02138 USA
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11
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Kéfi S, Miele V, Wieters EA, Navarrete SA, Berlow EL. How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience. PLoS Biol 2016; 14:e1002527. [PMID: 27487303 PMCID: PMC4972357 DOI: 10.1371/journal.pbio.1002527] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022] Open
Abstract
Species are linked to each other by a myriad of positive and negative interactions. This complex spectrum of interactions constitutes a network of links that mediates ecological communities' response to perturbations, such as exploitation and climate change. In the last decades, there have been great advances in the study of intricate ecological networks. We have, nonetheless, lacked both the data and the tools to more rigorously understand the patterning of multiple interaction types between species (i.e., "multiplex networks"), as well as their consequences for community dynamics. Using network statistical modeling applied to a comprehensive ecological network, which includes trophic and diverse non-trophic links, we provide a first glimpse at what the full "entangled bank" of species looks like. The community exhibits clear multidimensional structure, which is taxonomically coherent and broadly predictable from species traits. Moreover, dynamic simulations suggest that this non-random patterning of how diverse non-trophic interactions map onto the food web could allow for higher species persistence and higher total biomass than expected by chance and tends to promote a higher robustness to extinctions.
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Affiliation(s)
- Sonia Kéfi
- Institut des Sciences de l’Evolution de Montpellier, BioDICée team, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Montpellier, France
| | - Vincent Miele
- Laboratoire Biométrie et Biologie Evolutive, CNRS, UMR5558, Université de Lyon, Villeurbanne, France
| | - Evie A. Wieters
- Estación Costera de Investigaciones Marinas (ECIM), Center for Marine Conservation, LINC-Global, Chile
| | - Sergio A. Navarrete
- Estación Costera de Investigaciones Marinas (ECIM), Center for Marine Conservation, LINC-Global, Chile
- Center for Applied Ecology and Sustainability (CAPES), Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eric L. Berlow
- Vibrant Data Inc., San Francisco, California, United States of America
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Port JA, O'Donnell JL, Romero‐Maraccini OC, Leary PR, Litvin SY, Nickols KJ, Yamahara KM, Kelly RP. Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Mol Ecol 2016; 25:527-41. [PMID: 26586544 PMCID: PMC4737306 DOI: 10.1111/mec.13481] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/10/2015] [Accepted: 11/12/2015] [Indexed: 01/08/2023]
Abstract
Preserving biodiversity is a global challenge requiring data on species' distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species' distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource-intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species' eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false-negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.
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Affiliation(s)
- Jesse A. Port
- Center for Ocean SolutionsStanford UniversityStanfordCA94305USA
| | - James L. O'Donnell
- School of Marine and Environmental AffairsUniversity of WashingtonSeattleWA98105USA
| | | | - Paul R. Leary
- Hopkins Marine StationStanford UniversityPacific GroveCA93950USA
| | - Steven Y. Litvin
- Hopkins Marine StationStanford UniversityPacific GroveCA93950USA
| | - Kerry J. Nickols
- Hopkins Marine StationStanford UniversityPacific GroveCA93950USA
- California State UniversityMonterey BaySeasideCA93955USA
| | | | - Ryan P. Kelly
- School of Marine and Environmental AffairsUniversity of WashingtonSeattleWA98105USA
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