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McColl-Gausden EF, Weeks AR, Coleman R, Song S, Tingley R. Using hierarchical models to compare the sensitivity of metabarcoding and qPCR for eDNA detection. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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Carraro L, Blackman RC, Altermatt F. Modelling environmental DNA transport in rivers reveals highly resolved spatio-temporal biodiversity patterns. Sci Rep 2023; 13:8854. [PMID: 37258598 DOI: 10.1038/s41598-023-35614-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity.
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Affiliation(s)
- Luca Carraro
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland.
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland.
| | - Rosetta C Blackman
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland
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Hauck LL, Atkinson CL, Homyack JA, Penaluna BE, Mangum C, Coble AA, Nettles J, Thornton-Frost JE, Fix MJ. Molecular identity crisis: environmental DNA metabarcoding meets traditional taxonomy—assessing biodiversity and freshwater mussel populations (Unionidae) in Alabama. PeerJ 2023; 11:e15127. [PMID: 37033728 PMCID: PMC10078462 DOI: 10.7717/peerj.15127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/04/2023] [Indexed: 04/05/2023] Open
Abstract
The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat Pleurobema decisum and P. chattanoogaense as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that Fusconaia flava and F. cerina are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay.
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Affiliation(s)
- Laura L. Hauck
- Pacific Northwest Research Station, U.S. Department of Agriculture, Forest Service, Corvallis, OR, USA
| | - Carla L. Atkinson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | | | - Brooke E. Penaluna
- Pacific Northwest Research Station, U.S. Department of Agriculture, Forest Service, Corvallis, OR, USA
| | | | - Ashley A. Coble
- National Council for Air and Stream Improvement (NCASI), Corvallis, OR, USA
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Integrated Population Models: Achieving Their Potential. JOURNAL OF STATISTICAL THEORY AND PRACTICE 2023. [DOI: 10.1007/s42519-022-00302-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
AbstractPrecise and accurate estimates of abundance and demographic rates are primary quantities of interest within wildlife conservation and management. Such quantities provide insight into population trends over time and the associated underlying ecological drivers of the systems. This information is fundamental in managing ecosystems, assessing species conservation status and developing and implementing effective conservation policy. Observational monitoring data are typically collected on wildlife populations using an array of different survey protocols, dependent on the primary questions of interest. For each of these survey designs, a range of advanced statistical techniques have been developed which are typically well understood. However, often multiple types of data may exist for the same population under study. Analyzing each data set separately implicitly discards the common information contained in the other data sets. An alternative approach that aims to optimize the shared information contained within multiple data sets is to use a “model-based data integration” approach, or more commonly referred to as an “integrated model.” This integrated modeling approach simultaneously analyzes all the available data within a single, and robust, statistical framework. This paper provides a statistical overview of ecological integrated models, with a focus on integrated population models (IPMs) which include abundance and demographic rates as quantities of interest. Four main challenges within this area are discussed, namely model specification, computational aspects, model assessment and forecasting. This should encourage researchers to explore further and develop new practical tools to ensure that full utility can be made of IPMs for future studies.
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Dominant barriers and the solutions to the social application of environmental DNA. LANDSCAPE AND ECOLOGICAL ENGINEERING 2023. [DOI: 10.1007/s11355-023-00549-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Yoshioka A, Mitamura T, Matsuki N, Shimizu A, Ouchi H, Oguma H, Jo J, Fukasawa K, Kumada N, Jingu S, Tabuchi K. Camera-trapping estimates of the relative population density of Sympetrum dragonflies: application to multihabitat users in agricultural landscapes. PeerJ 2023; 11:e14881. [PMID: 36874968 PMCID: PMC9983425 DOI: 10.7717/peerj.14881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/20/2023] [Indexed: 03/06/2023] Open
Abstract
Although camera trapping has been effectively used for wildlife monitoring, its application to multihabitat insects (i.e., insects requiring terrestrial and aquatic ecosystems) is limited. Among such insects, perching dragonflies of the genus Sympetrum (darter dragonflies) are agroenvironmental indicators that substantially contribute to agricultural biodiversity. To examine whether custom-developed camera traps for perching dragonflies can be used to assess the relative population density of darter dragonflies, camera trapping, a line-transect survey of mature adult dragonflies, and a line-transect survey of exuviae were conducted for three years in rice paddy fields in Japan. The detection frequency of camera traps in autumn was significantly correlated with the density index of mature adults recorded during the transect surveys in the same season for both Sympetrum infuscatum and other darter species. In analyses of camera-detection frequency in autumn and exuviae in early summer, a significant correlation was observed between the camera-detection frequency of mature adults and the exuviae-density index in the following year for S. infuscatum; however, a similar correlation was not observed for other darter species. These results suggest that terrestrial camera trapping has the potential to be effective for monitoring the relative density of multihabitat users such as S. infuscatum, which shows frequent perching behavior and relatively short-distance dispersal.
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Affiliation(s)
- Akira Yoshioka
- Fukushima Regional Collaborative Research Center, National Institute for Environmental Studies, Miharu, Tamura-gun, Fukushima, Japan
| | - Toshimasa Mitamura
- Hama-dori Research Centre, Fukushima Agricultural Technology Centre, Soma, Fukushima, Japan
| | - Nobuhiro Matsuki
- Aizu Research Centre, Fukushima Agricultural Technology Centre, Aizubange, Fukushima, Japan
| | | | - Hirofumi Ouchi
- Fukushima Regional Collaborative Research Center, National Institute for Environmental Studies, Miharu, Tamura-gun, Fukushima, Japan
| | - Hiroyuki Oguma
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Jaeick Jo
- Fukushima Regional Collaborative Research Center, National Institute for Environmental Studies, Miharu, Tamura-gun, Fukushima, Japan
| | - Keita Fukasawa
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Nao Kumada
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Shoma Jingu
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Ken Tabuchi
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate, Japan
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Tercel MPTG, Cuff JP. The complex epistemological challenge of data curation in dietary metabarcoding: Comment on "The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation" by Littleford-Colquhoun et al. (2022). Mol Ecol 2022; 31:5653-5659. [PMID: 35778947 DOI: 10.1111/mec.16576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 01/13/2023]
Abstract
In their article, Littleford-Colquhoun et al. (2022) advise against using arbitrary relative read abundance (RRA) thresholds (i.e., minimum sequence copy thresholds) for removing low-abundance sequences since they can increase false negative rates in dietary DNA metabarcoding data sets. The main criticisms presented against these widespread methods are that they (i) are arbitrary, often existing as standard values or defined based on researcher-selected delineations, (ii) are subjective, varying between studies and contexts, and, most problematically, (iii) result in the exclusion of true positives, particularly rarely consumed taxa, to the detriment of ecological insight. We commend the authors for presenting a refreshing and timely perspective on this often neglected topic, which is certainly in need of greater discussion following over a decade of significant advances in dietary metabarcoding. In this complex epistemological problem of false positives versus false negatives, we feel that several of the points raised deserve additional discussion. We address these aspects below, including measured approaches to data filtration and consistent representation of RRAs, and we welcome any further discourse to solidify or refute the concepts therein.
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Affiliation(s)
- Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, UK.,Durrell Wildlife Conservation Trust, Trinity, Jersey, Channel Islands
| | - Jordan P Cuff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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