| Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb
Keck, F., & Altermatt, F. (2023). Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb. Molecular Ecology Resources, 23(2), 511-518. https://doi.org/10.1111/1755-0998.13723 |
| Homogeneity in terrestrial land cover is reflected in fish diversity patterns in a Chinese river system
Kirschner, D., Zhang, Y., Zhong, W., Zhang, X., Pellissier, L., & Altermatt, F. (2023). Homogeneity in terrestrial land cover is reflected in fish diversity patterns in a Chinese river system. Environmental DNA, 5(6), 1679-1690. https://doi.org/10.1002/edn3.480 |
| Towards a genetic theory of island biogeography: inferring processes from multidimensional community-scale data
Overcast, I., Achaz, G., Aguilée, R., Andújar, C., Arribas, P., Creedy, T. J., … Morlon, H. (2023). Towards a genetic theory of island biogeography: inferring processes from multidimensional community-scale data. Global Ecology and Biogeography, 32(1), 4-23. https://doi.org/10.1111/geb.13604 |
| 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 |
| A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers
Keck, F., Hürlemann, S., Locher, N., Stamm, C., Deiner, K., & Altermatt, F. (2022). A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers. Metabarcoding and Metagenomics, 6, 117-131. https://doi.org/10.3897/mbmg.6.79351 |
| Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment
Keck, F., Blackman, R. C., Bossart, R., Brantschen, J., Couton, M., Hürlemann, S., … Altermatt, F. (2022). Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Molecular Ecology, 31(6), 1820-1835. https://doi.org/10.1111/mec.16364 |
| Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses
Keck, F., Couton, M., & Altermatt, F. (2022). Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses. Molecular Ecology Resources, 23(4), 742-755. https://doi.org/10.1111/1755-0998.13746 |
| 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 |
| High-throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds
Briscoe, A. G., Nichols, S., Hartikainen, H., Knipe, H., Foster, R., Green, A. J., … Bass, D. (2021). High-throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds. Molecular Ecology Resources, 22(4), 1303-1318. https://doi.org/10.1111/1755-0998.13548 |
| Assessing the impact of the threatened crucian carp (<em>Carassius carassius</em>) on pond invertebrate diversity: A comparison of conventional and molecular tools
Harper, L. R., Lawson Handley, L., Sayer, C. D., Read, D. S., Benucci, M., Blackman, R. C., … Hänfling, B. (2021). Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity: A comparison of conventional and molecular tools. Molecular Ecology, 30, 3252-3269. https://doi.org/10.1111/mec.15670 |
| Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, <em>Dreissena rostriformis bugensis</em> in flowing water
Blackman, R. C., Ling, K. K. S., Harper, L. R., Shum, P., Hänfling, B., & Lawson-Handley, L. (2020). Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water. Ecology and Evolution, 10(23), 13248-13259. https://doi.org/10.1002/ece3.6921 |
| Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring
Pawlowski, J., Apothéloz-Perret-Gentil, L., & Altermatt, F. (2020). Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring. Molecular Ecology, 29(22), 4258-4264. https://doi.org/10.1111/mec.15643 |
| How does environmental inter-annual variability shape aquatic microbial communities? A 40-year annual record of sedimentary DNA from a boreal Lake (Nylandssjön, Sweden)
Capo, E., Rydberg, J., Tolu, J., Domaizon, I., Debroas, D., Bindler, R., & Bigler, C. (2019). How does environmental inter-annual variability shape aquatic microbial communities? A 40-year annual record of sedimentary DNA from a boreal Lake (Nylandssjön, Sweden). Frontiers in Ecology and Evolution, 7, 245 (13 pp.). https://doi.org/10.3389/fevo.2019.00245 |
| Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds
Harper, L. R., Buxton, A. S., Rees, H. C., Bruce, K., Brys, R., Halfmaerten, D., … Hänfling, B. (2019). Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia, 826(1), 25-41. https://doi.org/10.1007/s10750-018-3750-5 |
| Assessing different components of diversity across a river network using eDNA
Mächler, E., Little, C. J., Wüthrich, R., Alther, R., Fronhofer, E. A., Gounand, I., … Altermatt, F. (2019). Assessing different components of diversity across a river network using eDNA. Environmental DNA, 1(3), 290-301. https://doi.org/10.1002/edn3.33 |
| Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program
Lefrançois, E., Apothéloz-Perret-Gentil, L., Blancher, P., Botreau, S., Chardon, C., Crepin, L., … Bouchez, A. (2018). Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program. Environmental Science and Pollution Research, 25(34), 33858-33866. https://doi.org/10.1007/s11356-018-2172-2 |
| The ecologist's field guide to sequence-based identification of biodiversity
Creer, S., Deiner, K., Frey, S., Porazinska, D., Taberlet, P., Thomas, W. K., … Bik, H. M. (2016). The ecologist's field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution, 7, 1008-1018. https://doi.org/10.1111/2041-210X.12574 |