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Large‐scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases
Sieber, N., King, A., Krieg, R., Zenker, A., Vorburger, C., & Hartikainen, H. (2024). Large‐scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases. Environmental DNA, 6(1), e427 (14 pp.). https://doi.org/10.1002/edn3.427
Molecular metrics to monitor ecological status of large rivers: implementation of diatom DNA metabarcoding in the Joint Danube Survey 4
Tapolczai, K., Chonova, T., Fidlerová, D., Makovinská, J., Mora, D., Weigand, A., & Zimmermann, J. (2024). Molecular metrics to monitor ecological status of large rivers: implementation of diatom DNA metabarcoding in the Joint Danube Survey 4. Ecological Indicators, 160, 111883 (13 pp.). https://doi.org/10.1016/j.ecolind.2024.111883
Detection of fish sedimentary DNA in aquatic systems: a review of methodological challenges and future opportunities
Huston, G. P., Lopez, M. L. D., Cheng, Y., King, L., Duxbury, L. C., Picard, M., … Capo, E. (2023). Detection of fish sedimentary DNA in aquatic systems: a review of methodological challenges and future opportunities. Environmental DNA, 5(6), 1449-1472. https://doi.org/10.1002/edn3.467
A combination of machine-learning and eDNA reveals the genetic signature of environmental change at the landscape levels
Keck, F., Brantschen, J., & Altermatt, F. (2023). A combination of machine-learning and eDNA reveals the genetic signature of environmental change at the landscape levels. Molecular Ecology, 32(17), 4791-4800. https://doi.org/10.1111/mec.17073
Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes
Reji Chacko, M., Altermatt, F., Fopp, F., Guisan, A., Keggin, T., Lyet, A., … Pellissier, L. (2023). Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes. Oecologia, 202, 699-713. https://doi.org/10.1007/s00442-023-05428-4
Using eDNA to understand predator–prey interactions influenced by invasive species
Riaz, M., Warren, D., Wittwer, C., Cocchiararo, B., Hundertmark, I., Reiners, T. E., … Nowak, C. (2023). Using eDNA to understand predator–prey interactions influenced by invasive species. Oecologia, 202(4), 757-767. https://doi.org/10.1007/s00442-023-05434-6
A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA
Zhang, H., Mächler, E., Morsdorf, F., Niklaus, P. A., Schaepman, M. E., & Altermatt, F. (2023). A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA. Science of the Total Environment, 867, 161365 (12 pp.). https://doi.org/10.1016/j.scitotenv.2022.161365
Gap analysis for DNA-based biomonitoring of aquatic ecosystems in China
Li, F., Zhang, Y., Altermatt, F., Zhang, X., Cai, Y., & Yang, Z. (2022). Gap analysis for DNA-based biomonitoring of aquatic ecosystems in China. Ecological Indicators, 137, 108732 (11 pp.). https://doi.org/10.1016/j.ecolind.2022.108732
Environmental DNA metabarcoding for benthic monitoring: a review of sediment sampling and DNA extraction methods
Pawlowski, J., Bruce, K., Panksep, K., Aguirre, F. I., Amalfitano, S., Apothéloz-Perret-Gentil, L., … Fazi, S. (2022). Environmental DNA metabarcoding for benthic monitoring: a review of sediment sampling and DNA extraction methods. Science of the Total Environment, 818, 151783 (17 pp.). https://doi.org/10.1016/j.scitotenv.2021.151783
Parasite DNA detection in water samples enhances crayfish plague monitoring in asymptomatic invasive populations
Sieber, N., Hartikainen, H., Krieg, R., Zenker, A., & Vorburger, C. (2022). Parasite DNA detection in water samples enhances crayfish plague monitoring in asymptomatic invasive populations. Biological Invasions, 24, 281-297. https://doi.org/10.1007/s10530-021-02644-y
How to design optimal eDNA sampling strategies for biomonitoring in river networks
Carraro, L., Stauffer, J. B., & Altermatt, F. (2021). How to design optimal eDNA sampling strategies for biomonitoring in river networks. Environmental DNA, 3(1), 157-172. https://doi.org/10.1002/edn3.137
Decision-making and best practices for taxonomy-free environmental DNA metabarcoding in biomonitoring using Hill numbers
Mächler, E., Walser, J. C., & Altermatt, F. (2021). Decision-making and best practices for taxonomy-free environmental DNA metabarcoding in biomonitoring using Hill numbers. Molecular Ecology, 30(13), 3326-3339. https://doi.org/10.1111/mec.15725
Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
Polanco F., A., Richards, E., Flück, B., Valentini, A., Altermatt, F., Brosse, S., … Pellissier, L. (2021). Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems. Environmental DNA, 3(6), 1113-1127. https://doi.org/10.1002/edn3.232
DNA metabarcoding reveals differences in distribution patterns and ecological preferences among genetic variants within some key freshwater diatom species
Pérez-Burillo, J., Trobajo, R., Leira, M., Keck, F., Rimet, F., Sigró, J., & Mann, D. G. (2021). DNA metabarcoding reveals differences in distribution patterns and ecological preferences among genetic variants within some key freshwater diatom species. Science of the Total Environment, 798, 149029 (17 pp.). https://doi.org/10.1016/j.scitotenv.2021.149029
Combining environmental DNA and species distribution modeling to evaluate reintroduction success of a freshwater fish
Riaz, M., Kuemmerlen, M., Wittwer, C., Cocchiararo, B., Khaliq, I., Pfenninger, M., & Nowak, C. (2020). Combining environmental DNA and species distribution modeling to evaluate reintroduction success of a freshwater fish. Ecological Applications, 30(2), e02034 (11 pp.). https://doi.org/10.1002/eap.2034
Validation of an eDNA-based method for the detection of wildlife pathogens in water
Sieber, N., Hartikainen, H., & Vorburger, C. (2020). Validation of an eDNA-based method for the detection of wildlife pathogens in water. Diseases of Aquatic Organisms, 141, 171-184. https://doi.org/10.3354/dao03524
Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments
Blackman, R. C., Mächler, E., Altermatt, F., Arnold, A., Beja, P., Boets, P., … Deiner, K. (2019). Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments. Metabarcoding and Metagenomics, 3, 49-57. https://doi.org/10.3897/mbmg.3.34735
Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)
Harper, L. R., Griffiths, N. P., Lawson Handley, L., Sayer, C. D., Read, D. S., Harper, K. J., … Hänfling, B. (2018). Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius). Freshwater Biology, 93-107. https://doi.org/10.1111/fwb.13197
The future of biotic indices in the ecogenomic era: integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
Pawlowski, J., Kelly-Quinn, M., Altermatt, F., Apothéloz-Perret-Gentil, L., Beja, P., Boggero, A., … Kahlert, M. (2018). The future of biotic indices in the ecogenomic era: integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Science of the Total Environment, 637-638, 1295-1310. https://doi.org/10.1016/j.scitotenv.2018.05.002
Tetracapsuloides bryosalmonae abundance in river water
Fontes, I., Hartikainen, H., Holland, J. W., Secombes, C. J., & Okamura, B. (2017). Tetracapsuloides bryosalmonae abundance in river water. Diseases of Aquatic Organisms, 124(2), 145-157. https://doi.org/10.3354/dao03116