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Coutant O, Jézéquel C, Mokany K, Cantera I, Covain R, Valentini A, Dejean T, Brosse S, Murienne J. Environmental DNA reveals a mismatch between diversity facets of Amazonian fishes in response to contrasting geographical, environmental and anthropogenic effects. GLOBAL CHANGE BIOLOGY 2023; 29:1741-1758. [PMID: 36408670 DOI: 10.1111/gcb.16533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/13/2022] [Indexed: 05/28/2023]
Abstract
Freshwater ecosystems are among the most endangered ecosystem in the world. Understanding how human activities affect these ecosystems requires disentangling and quantifying the contribution of the factors driving community assembly. While it has been largely studied in temperate freshwaters, tropical ecosystems remain challenging to study due to the high species richness and the lack of knowledge on species distribution. Here, the use of eDNA-based fish inventories combined to a community-level modelling approach allowed depicting of assembly rules and quantifying the relative contribution of geographic, environmental and anthropic factors to fish assembly. We then used the model predictions to map spatial biodiversity and assess the representativity of sites surveyed in French Guiana within the EU Water Framework Directive (WFD) and highlighted areas that should host unique freshwater fish assemblages. We demonstrated a mismatch between the taxonomic and functional diversity. Taxonomic assemblages between but also within basins were mainly the results of dispersal limitation resulting from basin isolation and natural river barriers. Contrastingly, functional assemblages were ruled by environmental and anthropic factors. The regional mapping of fish diversity indicated that the sites surveyed within the EU WFD had a better representativity of the regional functional diversity than taxonomic diversity. Importantly, we also showed that the assemblages expected to be the most altered by anthropic factors were the most poorly represented in terms of functional diversity in the surveyed sites. The predictions of unique functional and taxonomic assemblages could, therefore, guide the establishment of new survey sites to increase fish diversity representativity and improve this monitoring program.
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Affiliation(s)
- Opale Coutant
- Laboratoire Evolution et Diversité Biologique (UMR 5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Céline Jézéquel
- Laboratoire Evolution et Diversité Biologique (UMR 5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Karel Mokany
- CSIRO, Canberra, Australian Capital Territory, Australia
| | - Isabel Cantera
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy
| | - Raphaël Covain
- Department of Herpetology and Ichthyology, Museum of Natural History, Geneva, Switzerland
| | | | | | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique (UMR 5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR 5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
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Golpour A, Šmejkal M, Čech M, dos Santos RA, Souza AT, Jůza T, Martínez C, Bartoň D, Vašek M, Draštík V, Kolařík T, Kočvara L, Říha M, Peterka J, Blabolil P. Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.913279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.
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Flück B, Mathon L, Manel S, Valentini A, Dejean T, Albouy C, Mouillot D, Thuiller W, Murienne J, Brosse S, Pellissier L. Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem. Sci Rep 2022; 12:10247. [PMID: 35715444 PMCID: PMC9205931 DOI: 10.1038/s41598-022-13412-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/24/2022] [Indexed: 01/04/2023] Open
Abstract
High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA.
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Affiliation(s)
- Benjamin Flück
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland.
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| | - Laëtitia Mathon
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | | | - Camille Albouy
- DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro - Agrocampus Ouest, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes Cedex 3, France
| | - David Mouillot
- MARBEC, Univ. Montpellier,CNRS, IRD, Ifremer, Montpellier, France
- Institut Universitaire de France, IUF, 75231, Paris, France
| | - Wilfried Thuiller
- CNRS, LECA, Laboratoire d'Écologie Alpine, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, 38000, Grenoble, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Loïc Pellissier
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland.
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
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Cantera I, Decotte JB, Dejean T, Murienne J, Vigouroux R, Valentini A, Brosse S. Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach. Mol Ecol Resour 2021; 22:1274-1283. [PMID: 34724352 DOI: 10.1111/1755-0998.13544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022]
Abstract
Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species-rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species. eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with increasing distance between sites. The distance decay of similarity derived from eDNA was similar and even more pronounced than that obtained with capture-based methods (gill-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species. Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provides a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture-based methods, which describes fish fauna over a few hundred metres.
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Affiliation(s)
- Isabel Cantera
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III Paul Sabatier, Toulouse, France
| | | | - Tony Dejean
- Vigilife, Le Bourget-du-Lac, France.,Spygen, Le Bourget-du-Lac, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut, Hydreco, Kourou Cedex, French Guiana
| | | | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III Paul Sabatier, Toulouse, France
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de Santana CD, Parenti LR, Dillman CB, Coddington JA, Bastos DA, Baldwin CC, Zuanon J, Torrente-Vilara G, Covain R, Menezes NA, Datovo A, Sado T, Miya M. The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes. Sci Rep 2021; 11:18159. [PMID: 34518574 PMCID: PMC8438044 DOI: 10.1038/s41598-021-97128-3] [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: 04/23/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.
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Affiliation(s)
- C David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.
| | - Lynne R Parenti
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Casey B Dillman
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Douglas A Bastos
- Programa de Pós-Graduação em Ciências Biológicas (BADPI), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Carole C Baldwin
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Gislene Torrente-Vilara
- Instituto do Mar, Universidade Federal de São Paulo, Campus Baixada Santista, Santos, São Paulo, Brazil
| | - Raphaël Covain
- Museum of Natural History, Department of Herpetology and Ichthyology, route de Malagnou 1, PO Box 6434, 1211, Geneva 6, Switzerland
| | - Naércio A Menezes
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - Aléssio Datovo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - T Sado
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
| | - M Miya
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
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Papa Y, Le Bail PY, Covain R. Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin. Mol Ecol Resour 2021; 21:2109-2124. [PMID: 33892518 DOI: 10.1111/1755-0998.13402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/27/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.
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Affiliation(s)
- Yvan Papa
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | - Raphaël Covain
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland
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