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Harwell LC, McMillion CA, Lamper AM, Summers JK. Development of a generalized pseudo-probabilistic approach for characterizing ecological conditions in estuaries using secondary data. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:753. [PMID: 39030312 PMCID: PMC11271375 DOI: 10.1007/s10661-024-12877-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/28/2024] [Indexed: 07/21/2024]
Abstract
Under the best circumstances, achieving or sustaining optimum ecological conditions in estuaries is challenging. Persistent information gaps in estuarine data make it difficult to differentiate natural variability from potential regime shifts. Long-term monitoring is critical for tracking ecological change over time. In the United States (US), many resource management programs are working at maximum capacity to address existing state and federal water quality mandates (e.g., pollutant load limits, climate impact mitigation, and fisheries management) and have little room to expand routine sampling efforts to conduct periodic ecological baseline assessments, especially at state and local scales. Alternative design, monitoring, and assessment approaches are needed to help offset the burden of addressing additional data needs to increase understanding about estuarine system resilience when existing monitoring data are sparse or spatially limited. Research presented here offers a pseudo-probabilistic approach that allows for the use of found or secondary data, such as data on hand and other acquired data, to generate statistically robust characterizations of ecological conditions in estuaries. Our approach uses a generalized pseudo-probabilistic framework to synthesize data from different contributors to inform probabilistic-like baseline assessments. The methodology relies on simple geospatial techniques and existing tools (R package functions) developed for the US Environmental Protection Agency to support ecological monitoring and assessment programs like the National Coastal Condition Assessment. Using secondary estuarine water quality data collected in the Northwest Florida (US) estuaries, demonstrations suggest that the pseudo-probabilistic approach produces estuarine condition assessment results with reasonable statistical confidence, improved spatial representativeness, and value-added information. While the pseudo-probabilistic framework is not a substitute for fully evolved monitoring, it offers a scalable alternative to bridge the gap between limitations in resource management capability and optimal monitoring strategies to track ecological baselines in estuaries over time.
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Affiliation(s)
- Linda C Harwell
- US Environmental Protection Agency, 1 Sabine Island Drive, Gulf Breeze, FL, 32561, USA.
| | - Courtney A McMillion
- Oak Ridge Associated Universities, 1 Sabine Island Drive, Gulf Breeze, FL, 32561, USA
- Santa Rosa County Florida, Development Services Department, 6051 Old Bagdad Highway, Suite 202, Milton, FL, 32583, USA
| | - Andrea M Lamper
- Oak Ridge Associated Universities, 1 Sabine Island Drive, Gulf Breeze, FL, 32561, USA
- CDM Smith, 670 N Commercial St, Unit 208, Manchester, NH, 03101, USA
| | - J Kevin Summers
- US Environmental Protection Agency, 1 Sabine Island Drive, Gulf Breeze, FL, 32561, USA
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Jones LA, Domeier M. A Phanerozoic gridded dataset for palaeogeographic reconstructions. Sci Data 2024; 11:710. [PMID: 38951561 PMCID: PMC11217452 DOI: 10.1038/s41597-024-03468-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/03/2024] [Indexed: 07/03/2024] Open
Abstract
Global Plate Models are widely used in the Earth Sciences to reconstruct the past geographic position of geological and palaeontological samples. However, the application of Global Plate Models to retrieve 'palaeocoordinates' is not trivial. Different Global Plate Models exist which vary in their complexity, spatiotemporal coverage, reference frame, and intended use. Consequently, careful consideration of which models are appropriate for any given research question is required. Here, we document and provide access to reconstruction datasets for five Global Plate Models in the palaeomagnetic reference frame. These datasets provide 'true' palaeolatitudes for three discrete global grids reconstructed at one-million-year intervals throughout the Phanerozoic (540-0 Ma), offering three key benefits for the Earth Science community: (1) allow users to look up palaeocoordinates for their samples (e.g. fossil occurrences) through simple indexing without having to learn additional software packages; (2) provide palaeocoordinates which have been generated consistently with thorough documentation; (3) provide static files which preserve model output and which can be used to evaluate palaeogeographic differences between Global Plate Models.
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Affiliation(s)
- Lewis A Jones
- Centro de Investigación Mariña, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, Spain.
| | - Mathew Domeier
- Centre for Earth Evolution and Dynamics (CEED), University of Oslo, NO-0316, Oslo, Norway.
- Centre for Planetary Habitability (PHAB), University of Oslo, NO-0316, Oslo, Norway.
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Smith LM, Reschke EM, Bousquin JJ, Cheskiewicz LP, Ilias N, Summers JK, Harvey JE. Methods for a composite ecological suitability measure to inform cumulative restoration assessments in Gulf of Mexico estuaries. ECOLOGICAL INDICATORS 2023; 154:1-15. [PMID: 38274645 PMCID: PMC10807174 DOI: 10.1016/j.ecolind.2023.110896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Ecosystem management requires a systematic, holistic approach that considers ecological and social outcomes. Effective restoration practices promote a balance of ecological and social goals by addressing ecological integrity, efficiently maximizing benefits while minimizing investment, and encompassing collaborative stakeholder engagement. Socio-ecological assessments can inform adaptive management and be utilized to prioritize restoration activities and monitor restoration effectiveness. In estuarine systems, socio-ecological assessments should evaluate the ability of habitats to support both ecologically and locally important species. The composite measure presented utilizes a combination of ecological and social measures to characterize ecological suitability for individual and multiple Gulf of Mexico estuarine species. The ecological suitability value (ES) for a given spatial unit is based on a suite of biophysical measures of the quality and extent of suitable habitat for each species, the species' trophic importance in a food web context, and the importance of each species in relation to stakeholder values and benefits. ES values for individual spatial units can be aggregated to estimate the distribution of ecological suitability at the estuarine scale. The ES values are calculated using examples for each step in the process. The information provided by ecological suitability characterizations can support restoration prioritization decisions for Gulf of Mexico estuaries and can provide a baseline measure to gauge restoration effectiveness over time to inform cumulative restoration assessments.
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Affiliation(s)
- Lisa M. Smith
- U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecosystem Measurement and Modeling Division, 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA
| | - Erin M. Reschke
- U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecosystem Measurement and Modeling Division, 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA
| | - Justin J. Bousquin
- U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecosystem Measurement and Modeling Division, 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA
| | - Leonard P. Cheskiewicz
- U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecosystem Measurement and Modeling Division, 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA
| | - Nikolaos Ilias
- Oak Ridge Associated Universities (ORAU), 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA
- Advanced Environmental Technologies, 1318 Dunmire Street, Suite 1, Pensacola, FL 32504, USA
| | - J. Kevin Summers
- U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecosystem Measurement and Modeling Division, 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA
| | - James E. Harvey
- U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecosystem Measurement and Modeling Division, 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA
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Vasar M, Davison J, Moora M, Sepp SK, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Oja J, Garibay-Orijel R, Hiiesalu I, Koorem K, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Doležal J, Palacios AMV, Tedersoo L, Zobel M. Metabarcoding of soil environmental DNA to estimate plant diversity globally. FRONTIERS IN PLANT SCIENCE 2023; 14:1106617. [PMID: 37143888 PMCID: PMC10151745 DOI: 10.3389/fpls.2023.1106617] [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: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
Introduction Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.
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Affiliation(s)
- Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- *Correspondence: Martti Vasar,
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne, University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, WA, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jiři Doležal
- Institute of Botany, The Czech Academy of Sciences, Třeboň, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
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Research on Navigation Safety Evaluation of Coastal Waters Based on Dynamic Irregular Grid. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite being a minor probability event, marine accidents can cause serious consequences such as casualties, environmental damage, and even massive economic losses. As an important part of the marine traffic safety system, the evaluation of navigation safety in coastal waters is of great significance to ensure the safety of ship navigation. In order to objectively evaluate the safety of navigation, this paper proposes an irregular grid division method that combines influencing factors including seabed topography, ship traffic flow, electronic charts, and marine meteorology. In this work, the navigable boundary was extracted by spatial analysis algorithms of the slope calculation. Based on the alpha-shape algorithm and the Voronoi diagram, the constrained Delaunay triangulation was used to extract the inner and outer boundaries of the ship′s navigation area, and the time-varying factors of marine hydrology and meteorology were integrated to form a dynamic irregular grid. The navigation safety evaluation indicators in coastal waters were divided into five risk levels, namely lower, low, medium, high, and higher. Then, the entropy weight theory was used to calculate the weight of the evaluation index. Finally, a safety evaluation model was constructed to evaluate the risk of navigation safety in coastal waters. Herein, taking the coastal waters of Lianyungang Port as a demonstration area, this paper divided the dynamic irregular grid and conducted the navigation safety analysis and evaluation based on the grid. The experimental results show that our method fully considers the influence of objective factors and the uncertainty of safety evaluation indicators and has favorable adaptability to the evaluation of navigation safety in coastal waters.
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