Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate Zones
ABSTRACT Long‐term biological monitoring and management depend on efficient protocols and methodology to characterize and precisely describe species distributions and diversity. In recent years, environmental DNA has progressively become a tool of choice in survey programs. However, the effect of va...
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| Format: | Article |
| Language: | English |
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Wiley
2024-11-01
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| Series: | Environmental DNA |
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| Online Access: | https://doi.org/10.1002/edn3.70015 |
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| author | Erik García‐Machado Eric Normandeau Guillaume Côté Isabeau Caza‐Allard Charles Babin Louis Bernatchez |
| author_facet | Erik García‐Machado Eric Normandeau Guillaume Côté Isabeau Caza‐Allard Charles Babin Louis Bernatchez |
| author_sort | Erik García‐Machado |
| collection | DOAJ |
| description | ABSTRACT Long‐term biological monitoring and management depend on efficient protocols and methodology to characterize and precisely describe species distributions and diversity. In recent years, environmental DNA has progressively become a tool of choice in survey programs. However, the effect of variables such as sampling effort and sampling design still requires consideration. Simple random, grid, and transect‐based sampling methods are widely used in ecological surveys to obtain an unbiased estimation of species richness and community structure. However, under certain conditions where spatial information is available, sampling design and sequencing depth can be optimized to reduce effort and cost. Here, we evaluate different subsampling approaches to identify sampling strategies that are both easily implemented in the field and provide optimal recovery of species diversity for a given sampling effort. With a homogeneous grid‐based sampling (25–50 samples by lake) of 12 freshwater lakes in southeastern Québec, and using the 12S MiFish metabarcoding primer set, we demonstrate that random and stratified designs perform similarly to detect 90% and 95% of species. However, we found that, under certain circumstances, stratified sampling outperformed random sampling, requiring lower numbers of samples to detect the same species diversity. We also demonstrate that for the minimum sequence threshold and sample replication used in our study, a sequencing depth of 50K reads per sample is adequate to obtain a reliable portrayal of species richness. In this study, we contribute to the effort of eDNA sampling standardization by providing data for selecting the best sampling design, sequence depth, and sample size to detect 90%–95% of fish species found in temperate lakes. |
| format | Article |
| id | doaj-art-a48f66a5c1c840faa27fd20141d24273 |
| institution | Kabale University |
| issn | 2637-4943 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj-art-a48f66a5c1c840faa27fd20141d242732025-01-29T05:11:50ZengWileyEnvironmental DNA2637-49432024-11-0166n/an/a10.1002/edn3.70015Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate ZonesErik García‐Machado0Eric Normandeau1Guillaume Côté2Isabeau Caza‐Allard3Charles Babin4Louis Bernatchez5Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City Quebec CanadaPlateforme de bio‐informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes) Université Laval Quebec City Quebec CanadaMinistère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs Quebec City Quebec CanadaInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City Quebec CanadaInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City Quebec CanadaInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City Quebec CanadaABSTRACT Long‐term biological monitoring and management depend on efficient protocols and methodology to characterize and precisely describe species distributions and diversity. In recent years, environmental DNA has progressively become a tool of choice in survey programs. However, the effect of variables such as sampling effort and sampling design still requires consideration. Simple random, grid, and transect‐based sampling methods are widely used in ecological surveys to obtain an unbiased estimation of species richness and community structure. However, under certain conditions where spatial information is available, sampling design and sequencing depth can be optimized to reduce effort and cost. Here, we evaluate different subsampling approaches to identify sampling strategies that are both easily implemented in the field and provide optimal recovery of species diversity for a given sampling effort. With a homogeneous grid‐based sampling (25–50 samples by lake) of 12 freshwater lakes in southeastern Québec, and using the 12S MiFish metabarcoding primer set, we demonstrate that random and stratified designs perform similarly to detect 90% and 95% of species. However, we found that, under certain circumstances, stratified sampling outperformed random sampling, requiring lower numbers of samples to detect the same species diversity. We also demonstrate that for the minimum sequence threshold and sample replication used in our study, a sequencing depth of 50K reads per sample is adequate to obtain a reliable portrayal of species richness. In this study, we contribute to the effort of eDNA sampling standardization by providing data for selecting the best sampling design, sequence depth, and sample size to detect 90%–95% of fish species found in temperate lakes.https://doi.org/10.1002/edn3.70015environmental DNAfishsample design sequencing depthsampling optimization |
| spellingShingle | Erik García‐Machado Eric Normandeau Guillaume Côté Isabeau Caza‐Allard Charles Babin Louis Bernatchez Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate Zones Environmental DNA environmental DNA fish sample design sequencing depth sampling optimization |
| title | Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate Zones |
| title_full | Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate Zones |
| title_fullStr | Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate Zones |
| title_full_unstemmed | Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate Zones |
| title_short | Evaluating Sampling Designs to Survey Fish Diversity in Lakes From Northern Temperate Zones |
| title_sort | evaluating sampling designs to survey fish diversity in lakes from northern temperate zones |
| topic | environmental DNA fish sample design sequencing depth sampling optimization |
| url | https://doi.org/10.1002/edn3.70015 |
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