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Theis S, Chreston A, Wallace A, Graham B, Coey B, Little D, Cartwright L, Poesch M, Portiss R, Ruppert J. Nearshore fish community changes along the Toronto waterfront in accordance with management and restoration goals: Insights from two decades of monitoring. PLoS One 2024; 19:e0298333. [PMID: 38408042 PMCID: PMC10896508 DOI: 10.1371/journal.pone.0298333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Aquatic habitat in the Greater Toronto Area has been subject to anthropogenic stressors. The subsequent aquatic habitat degradation that followed led to the Toronto and Region waterfront being listed as an Area of Concern in 1987. Thus, extensive shoreline and riparian habitat restoration have been implemented as part of the Toronto and Region Remedial Action Plan in conjunction with local stakeholders, ministries, and NGOs in an overall effort to increase fish, bird, and wildlife habitat. A key aspect of current fish habitat restoration efforts, monitored by Toronto and Region Conservation Authority, is to account for long-term community changes within the target ecosystem to better understand overall changes at a larger spatial scale. Here we use electrofishing data from the past 20 years with over 100,000 records and across 72km of coastline to show how declines and fluctuations in fish biomass and catch along the waterfront are driven by a few individual species across three main ecotypes, such as coastal wetlands, embayments, and open coast sites, with the remaining species showing a high level of stability. Using community traits and composition for resident species we demonstrate native warmwater species have become more dominant along the waterfront in recent years, suggesting that restoration efforts are functioning as intended. Additionally, piscivore and specialist species have increased in their relative biomass contribution, approaching existing restoration targets. Altogether this waterfront-wide evaluation allows us to detect overall changes along the waterfront and can be beneficial to understand community changes at an ecosystem level when implementing and monitoring restoration projects.
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Affiliation(s)
- Sebastian Theis
- Fisheries and Aquatic Conservation Lab, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Alberta, Canada
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Andrea Chreston
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Angela Wallace
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Brian Graham
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Brynn Coey
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Don Little
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Lyndsay Cartwright
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Mark Poesch
- Fisheries and Aquatic Conservation Lab, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rick Portiss
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
| | - Jonathan Ruppert
- Toronto and Region Conservation Authority, Watershed Planning and Ecosystem Science, North York, Ontario, Canada
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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2
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Carvajal-Quintero J, Comte L, Giam X, Olden JD, Brose U, Erős T, Filipe AF, Fortin MJ, Irving K, Jacquet C, Larsen S, Ruhi A, Sharma S, Villalobos F, Tedesco PA. Scale of population synchrony confirms macroecological estimates of minimum viable range size. Ecol Lett 2023; 26:291-301. [PMID: 36468276 DOI: 10.1111/ele.14152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/11/2022]
Abstract
Global ecosystems are facing a deepening biodiversity crisis, necessitating robust approaches to quantifying species extinction risk. The lower limit of the macroecological relationship between species range and body size has long been hypothesized as an estimate of the relationship between the minimum viable range size (MVRS) needed for species persistence and the organismal traits that affect space and resource requirements. Here, we perform the first explicit test of this assumption by confronting the MVRS predicted by the range-body size relationship with an independent estimate based on the scale of synchrony in abundance among spatially separated populations of riverine fish. We provide clear evidence of a positive relationship between the scale of synchrony and species body size, and strong support for the MVRS set by the lower limit of the range-body size macroecological relationship. This MVRS may help prioritize first evaluations for unassessed or data-deficient taxa in global conservation assessments.
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Affiliation(s)
- Juan Carvajal-Quintero
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig, Leipzig, Germany.,Leipzig University, Leipzig, Germany
| | - Lise Comte
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Xingli Giam
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Julian D Olden
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig, Leipzig, Germany.,Institute of Biodiversity, Friedrich-Schiller-University Jena, Jena, Germany
| | - Tibor Erős
- Balaton Limnological Research Institute, ELKH, Tihany, Hungary
| | - Ana Filipa Filipe
- Forest Research Centre, School of Agriculture, University of Lisbon, Lisbon, Portugal.,Associate Laboratory TERRA, Lisbon, Portugal
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Katie Irving
- Department of Biology, Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Claire Jacquet
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Stefano Larsen
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy.,Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy
| | - Albert Ruhi
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Sapna Sharma
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Fabricio Villalobos
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, Veracruz, Mexico
| | - Pablo A Tedesco
- UMR EDB, IRD 253, CNRS 5174, UPS, Université Toulouse 3 Paul Sabatier, Toulouse, France
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3
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Rivera SF, Rimet F, Vasselon V, Vautier M, Domaizon I, Bouchez A. Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects. Mol Ecol Resour 2021; 22:1440-1453. [PMID: 34863036 DOI: 10.1111/1755-0998.13568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/22/2021] [Accepted: 11/25/2021] [Indexed: 01/04/2023]
Abstract
Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered water depends on the study scope and can rapidly become time consuming according to the number of samples that have to be processed. To avoid time allocated to filtration, passive DNA samplers have been used to recover fish eDNA from marine environments faster. In freshwater ecosystems, aquatic biofilms were used to catch eDNA from macroinvertebrates. Here, we test the capacity of aquatic biofilms to entrap fish eDNA in a large lake and, therefore, the possibility to perform fish eDNA metabarcoding from this matrix compared to the traditional fish eDNA approach from filtered water samples. Methodological aspects of the use of aquatic biofilms for fish eDNA metabarcoding (e.g. PCR replicates, biological replicates, bioinformatics pipeline, reference database and taxonomic assignment) were validated against a mock community. When using biofilms from habitats sheltered from wind and waves, biofilm and water approach provided similar inventories. Richness and diversity were comparable between both approaches. Approaches differed only for rare taxa. Our results illustrate the capacity of aquatic biofilms to act as passive eDNA samplers of fish eDNA and, therefore, the possibility to use biofilms to monitor fish communities efficiently from biofilms. Furthermore, our results open up avenues of research to study a diversity of biological groups (among which bioindicators as diatoms, macroinvertebrates and fish) from eDNA isolated from a single environmental matrix reducing sampling efforts, analysis time and costs.
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Affiliation(s)
- Sinziana F Rivera
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | - Frédéric Rimet
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | | | - Marine Vautier
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | - Isabelle Domaizon
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | - Agnès Bouchez
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
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4
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Reid SM, Haxton T, Gutowsky LFG. Boat-electrofishing transect location and flow levels: influence on riverine fish monitoring in non-wadeable habitats. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:680. [PMID: 34591192 DOI: 10.1007/s10661-021-09444-w] [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: 03/19/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Fisheries monitoring can be improved by studying the influence of gear selectivity, sampling design, and habitat conditions. We used boat-electrofishing data to investigate how sample unit placement (shoreline and channel transects) and sampling conditions (low and high flow years) affect detection of fishes in a highly regulated Ontario (Canada) river system. Species detection histories associated with a spatially replicated sampling design was fit to a Bayesian hierarchical site occupancy model for 14 fishes. Habitat (transect location) had a significant effect on detection probabilities (p) for all species, with shoreline sampling more likely to detect species than channel. Sampling year had a significant effect on detectability of six species. The relative influence of habitat and sampling year varied among species. Detection probabilities based on combined shoreline and channel transect data across both years ranged from 0.09 to 0.48 and were positively correlated to species abundance. High detection probabilities and precise occupancy estimates were associated with sunfish and bass abundant in shoreline habitats. Small-bodied species closely associated with the riverbed or exhibiting schooling behavior tended to be poorly detected. Power to detect future changes in species distribution is expected to differ based on habitat sampled, with greater power associated with shoreline boat-electrofishing. Detecting small to moderate changes is not likely for most species. The addition of channel transects did not improve the effectiveness of shoreline sampling. Improvements to the current design could be realized by reallocating sampling effort from channel to shoreline and testing different gear in deep (> 3 m) habitats.
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Affiliation(s)
- Scott M Reid
- Aquatic Research and Monitoring Section, Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, ON, K9L 1Z8, Canada.
| | - Tim Haxton
- Aquatic Research and Monitoring Section, Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, ON, K9L 1Z8, Canada
| | - Lee F G Gutowsky
- Aquatic Research and Monitoring Section, Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, ON, K9L 1Z8, Canada
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Erickson RA, Merkes CM, Mize EL. Sampling Designs for Landscape-level eDNA Monitoring Programs. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2019; 15:760-771. [PMID: 30963692 DOI: 10.1002/ieam.4155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/20/2018] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
Effective natural resources management requires accurate information about species distributions. Environmental DNA (eDNA) analysis is a commonly used method to determine species presence and distribution. However, when understanding eDNA-based distribution data, managers must contend with imperfect detection in collection samples and subsamples (i.e., molecular analyses) impacting their ability to detect species and estimate occurrence. Occurrence models can estimate 3 probabilities: occurrence, capture, and eDNA detection. However, most occurrence models do not. To quantify imperfect detection in rare versus common species, we examined multiple field capture and detection probabilities. We studied this with 3 objectives: Determine sample sizes required to detect eDNA given imperfect detection, determine sample sizes required to estimate eDNA capture parameters, and examine performance of a 3-level occurrence model. We found detecting eDNA in ≥1 sample at a site required ≤15 samples per site for common species, but detecting eDNA when looking for rare species required 45 to 90 samples per site. Our occurrence model recovered known parameters unless capture and detection probabilities were <0.2 where >100 samples per site and ≥8 molecular replicates were required. Our findings illustrate the importance of sample size and molecular replication for eDNA-based work. Integr Environ Assess Manag 2019;15:760-771. Published 2019. This article is a US Government work and is in the public domain in the USA.
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Affiliation(s)
- Richard A Erickson
- Upper Midwest Environmental Sciences Center, US Geological Survey, La Crosse, Wisconsin
| | - Christopher M Merkes
- Upper Midwest Environmental Sciences Center, US Geological Survey, La Crosse, Wisconsin
| | - Erica L Mize
- Whitney Genetics Laboratory, Midwest Fisheries Center, US Fish and Wildlife Service, Onalaska, Wisconsin
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Plough LV, Ogburn MB, Fitzgerald CL, Geranio R, Marafino GA, Richie KD. Environmental DNA analysis of river herring in Chesapeake Bay: A powerful tool for monitoring threatened keystone species. PLoS One 2018; 13:e0205578. [PMID: 30383750 PMCID: PMC6211659 DOI: 10.1371/journal.pone.0205578] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/27/2018] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as ‘river herring’), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations). Overall, the qPCR assay showed very high target specificity in lab trials, and was successful in detecting river herring for 11/12 Chesapeake Bay tributaries in spring 2015 and 2016, with 106 out of 445 samples exhibiting positive eDNA hits. We found a strong correlation between eDNA abundance and ichthyoplankton count data (Spearman’s Rho = 0.52), and Phi-tests (correlation of presence/absence data) showed higher correlation between eDNA and ichthyoplankton data (Phi = 0.45) than adult data (Phi = 0.35). Detection probability was significantly lower on western vs. eastern shore tributaries of Chesapeake Bay, and blueback herring and alewife were more likely detected on the western and eastern shores, respectively. Temporal patterns of eDNA abundance over the spring spawning season revealed that alewife were present in high abundances weeks ahead of blueback herring, which aligns with known differences in spawning behavior of the species. In summary, the eDNA abundance data corresponded well to other field methods and has great potential to assist future monitoring efforts of river herring abundance and habitat use.
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Affiliation(s)
- Louis V. Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
- * E-mail:
| | - Matthew B. Ogburn
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Catherine L. Fitzgerald
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Rose Geranio
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Gabriella A. Marafino
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Kimberly D. Richie
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
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Watkins CJ, Quist MC, Shepard BB, Ireland SC. Electrofishing Effort Requirements for Estimating Species Richness in the Kootenai River, Idaho. NORTHWEST SCIENCE 2016. [DOI: 10.3955/046.090.0310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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