Francois Keck

Quantitative Ecology Freshwater Biology Data Science

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Research

My research activities are focussed on the links between environmental variation and community dynamics in freshwater ecosystems and how human activities are reshaping aquatic biodiversity. A significant part of my work also involves developing ideas, methods and scientific principles to support environmental monitoring and management. Over the years, I have developed a broad spectrum of skills and expertise in data science including statistics, data mining and modelling to extract valuable knowledge and insights from complex ecological data.

Unraveling the processes shaping biodiversity

A large part of my research focuses on the relative role of environmental, spatial and historical processes in driving freshwater community assembly. Why do these species live here? How do they interact with each other and with their environment? What rules dictate the composition and dynamics of these communities across time and space? These questions are at the heart of ecology, and I am working to address them by combining the analysis of ecological data with the tools of modern ecoinformatics (statistical modeling, machine learning, phylogenetics, etc.).

Assessing the ecological impacts of human activities

Freshwater environments are among the most threatened habitats on our planet. My work seeks to identify how human activities and global change are modifying biological communities and impacting the functioning of these vulnerable ecosystems. Measuring and understanding the mechanisms by which human activities modify environments and impact biodiversity are key elements in tackling the major environmental crisis we are currently experiencing.

Environmental DNA: a new perspective on biodiversity

Environmental DNA is a revolution and plays a central role in my research. My work on the methodological aspect of eDNA mainly focuses on bioinformatics and the use of genetic data for studying and monitoring biodiversity. I am particularly interested in the issue of reference databases, which provide a link between genetic sequences and taxonomy and constitute a central element in the processing of metabarcoding data.

Large scale ecological syntheses

In the face of the ongoing ecological crisis, the imperative for synthesis in ecology has become more pressing than ever. However, such synthesis can only be achieved through the integration of vast amounts of mostly scattered information and data. I'm interested in taking up this challenge on a wide range of ecological questions. Through the development of innovative new methodologies, I also wish to show that a new level of quantitative synthesis of the available knowledge in ecology can be achieved.

Publications

Featured Publications

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). Molecular Ecology.

Statistical models trained on raw eDNA can discriminate between reference and impacted environments. Check out our article in Molecular Ecology.

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Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Keck, F. et al. (2022). Molecular Ecology.

The first global meta-analysis of studies comparing traditional methods and DNA metabarcoding shows that richness estimates are globally consistent between approaches but species composition and identity can strongly differ.

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Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA

Keck, F. et al. (2020). Nature Communications.

Long-term sediment DNA analysis of 48 lakes reveals how anthropogenic pressures have drastically altered and homogenized microbial community diversity since the 19th century.

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Full List of Publications

[40] Impacts of diffuse urban stressors on stream benthic communities and ecosystem functioning: A review

Colls, M., Viza, A., Zufiarre, A., Camacho-Santamans, A., Laini, A., González-Ferreras, A. M., Filipe, A. F., Pérez-Calpe, A. V., Freixa, A., Lupon, A., Santamans, A. C., Pradhan, A., Espinosa, C., Vera-Trujillo, C., Gutiérrez-Cánovas, C., Mendoza-Lera, C., Bruno, D., Mercado-Bettin, D., Morant, D., Batista, D., Cunillera-Montcusi, D., Graça, D., Vico-Oton, E., Estévez, E., Leon-Palmero, E., Suarez, E. L., Fenoy, E., Lima, E., Picazo, F., Oficialdegui, F. J., Keck, F., Gionchetta, G., Sabas, I., Pérez-Silos, I., Antunes, I., Alvarez-Manzaneda, I., De Guzmán, I., Fernandes, I., Pereira Da Silva, J., Wei, J., Montes-Pérez, J. J., Trabulo, J., Ledesma, J. L. J., Fernandez-Calero, J. M., Ramião, J. P., Rubio-Rios, J., Gonzalez-Trujillo, J. D., Barral-Fraga, L., Jiménez, L., Vendrell-Puigmitja, L., Bertrans, L., Gomez-Gener, L., Rovelli, L., Thuile-Bistarelli, L., Sanchez-Morales, M., Cabrerizo, M. J., Aranguren-Gassis, M., Argudo, M., Navarro-Ramos, M. J., Atristain, M., Lopez-Rojo, N., Valiente, N., Perujo, N., Pereda, O., Llanos-Paez, O., Belmar, O., Tascon-Peña, O., Rodriguez-Lozano, P., Sánchez De Pedro, R., Arias-Real, R., Bolpagni, R., Del Campo, R., Poblador, S., Guareschi, S., Hilgert, S., Duarte, S., Rodriguez-Castillo, T., Chonova, T., Conejo-Orosa, T., Céspedes, V., Granados, V., Osorio, V., Vázquez, V., Martin-Vélez, V., Romero, F. (2024). Limnetica, 43(1), 1.

[39] Environmental DNA: The next chapter

Blackman, R., Couton, M., Keck, F., Kirschner, D., Carraro, L., Cereghetti, E., Perrelet, K., Bossart, R., Brantschen, J., Zhang, Y., Altermatt, F. (2024). Molecular Ecology, e17355.

[38] Measuring the state of aquatic environments using eDNA—upscaling spatial resolution of biotic indices

Blackman, R. C., Carraro, L., Keck, F., Altermatt, F. (2024). Philosophical Transactions of the Royal Society B: Biological Sciences, 379(1904), 20230121.

[37] Habitat suitability models reveal the spatial signal of environmental DNA in riverine networks

Brantschen, J., Fopp, F., Adde, A., Keck, F., Guisan, A., Pellissier, L., Altermatt, F. (2024). Ecography, n/a(n/a), e07267.

[36] Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

Keck, F., Altermatt, F. (2023). Molecular Ecology Resources, 23(2), 511-518.

[35] Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

Keck, F., Couton, M., Altermatt, F. (2023). Molecular Ecology Resources, 23(4), 742-755.

[34] Filling reference libraries with diatom environmental sequences: strengths and weaknesses

Kochoska, H., Chardon, C., Chonova, T., Keck, F., Kermarrec, L., Larras, F., Lefrancois, E., Rivera, S. F., Tapolczai, K., Vasselon, V., Levkov, Z., Rimet, F. (2023). Diatom Research, 38(2), 103-127.

[33] 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). Molecular Ecology, 32(17), 4791-4800.

[32] Revisiting global diversity and biogeography of freshwater diatoms: New insights from molecular data

Chonova, T., Rimet, F., Bouchez, A., Kahlert, M., Schneider, S. C., Bailet, B., Eulin-Garrigue, A., Gassiole, G., Monnier, O., Ouattara, A., Rey, S., Rhoné, M., Keck, F. (2023). Environmental DNA, 5(6), 1505-1515.

[31] Biodiversity patterns of Arctic diatom assemblages in lakes and streams: Current reference conditions and historical context for biomonitoring

Kahlert, M., Rühland, K. M., Lavoie, I., Keck, F., Saulnier‐Talbot, E., Bogan, D., Brua, R. B., Campeau, S., Christoffersen, K. S., Culp, J. M., Karjalainen, S. M., Lento, J., Schneider, S. C., Shaftel, R., Smol, J. P. (2022). Freshwater Biology, 67(1), 116-140.

[30] Ecological correlates of riverine diatom and macroinvertebrate alpha and beta diversity across Arctic Fennoscandia

Brittain, J. E., Heino, J., Friberg, N., Aroviita, J., Kahlert, M., Karjalainen, S.‐M., Keck, F., Lento, J., Liljaniemi, P., Mykrä, H., Schneider, S. C., Ylikörkkö, J. (2022). Freshwater Biology, 67(1), 49-63.

[29] 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., Kirschner, D., Locher, N., Zhang, H., Altermatt, F. (2022). Molecular Ecology, 31(6), 1820-1835.

[28] Paleoreconstructions of ciliate communities reveal long-term ecological changes in temperate lakes

Barouillet, C., Vasselon, V., Keck, F., Millet, L., Etienne, D., Galop, D., Rius, D., Domaizon, I. (2022). Scientific Reports, 12(1), 7899.

[27] 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). Metabarcoding and Metagenomics, 6, e79351.

[26] Co-occurrence, ecological profiles and geographical distribution based on unique molecular identifiers of the common freshwater diatoms Fragilaria and Ulnaria

Kahlert, M., Maaria Karjalainen, S., Keck, F., Kelly, M., Ramon, M., Rimet, F., Schneider, S., Tapolczai, K., Zimmermann, J. (2022). Ecological Indicators, 141, 109114.

[25] Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

Cordier, T., Alonso‐Sáez, L., Apothéloz‐Perret‐Gentil, L., Aylagas, E., Bohan, D. A., Bouchez, A., Chariton, A., Creer, S., Frühe, L., Keck, F., Keeley, N., Laroche, O., Leese, F., Pochon, X., Stoeck, T., Pawlowski, J., Lanzén, A. (2021). Molecular Ecology, 30(13), 2937-2958.

[24] The potential of exact sequence variants (ESVs) to interpret and assess the impact of agricultural pressure on stream diatom assemblages revealed by DNA metabarcoding

Tapolczai, K., Selmeczy, G. B., Szabó, B., B-Béres, V., Keck, F., Bouchez, A., Rimet, F., Padisák, J. (2021). Ecological Indicators, 122, 107322.

[23] 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). Science of The Total Environment, 798, 149029.

[22] Key Questions for Next-Generation Biomonitoring

Makiola, A., Compson, Z. G., Baird, D. J., Barnes, M. A., Boerlijst, S. P., Bouchez, A., Brennan, G., Bush, A., Canard, E., Cordier, T., Creer, S., Curry, R. A., David, P., Dumbrell, A. J., Gravel, D., Hajibabaei, M., Hayden, B., van der Hoorn, B., Jarne, P., Jones, J. I., Karimi, B., Keck, F., Kelly, M., Knot, I. E., Krol, L., Massol, F., Monk, W. A., Murphy, J., Pawlowski, J., Poisot, T., Porter, T. M., Randall, K. C., Ransome, E., Ravigné, V., Raybould, A., Robin, S., Schrama, M., Schatz, B., Tamaddoni-Nezhad, A., Trimbos, K. B., Vacher, C., Vasselon, V., Wood, S., Woodward, G., Bohan, D. A. (2020). Frontiers in Environmental Science, 7.

[21] Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA

Keck, F., Millet, L., Debroas, D., Etienne, D., Galop, D., Rius, D., Domaizon, I. (2020). Nature Communications, 11(1), 3831.

[20] Handling biological sequences in R with the bioseq package

Keck, F. (2020). Methods in Ecology and Evolution, 11(12), 1728-1732.

[19] Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

Chonova, T., Kurmayer, R., Rimet, F., Labanowski, J., Vasselon, V., Keck, F., Illmer, P., Bouchez, A. (2019). Frontiers in Microbiology, 10.

[18] Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status

Bailet, B., Bouchez, A., Franc, A., Frigerio, J.-M., Keck, F., Karjalainen, S.-M., Rimet, F., Schneider, S., Kahlert, M. (2019). Metabarcoding and Metagenomics, 3, e34002.

[17] Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)

Kahlert, M., Kelly, M. G., Mann, D. G., Rimet, F., Sato, S., Bouchez, A., Keck, F., Kroth, P. (2019). Journal of Phycology, 55(4), 948-970.

[16] Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms

Keck, F., Kahlert, M. (2019). Scientific Reports, 9(1), 1-8.

[15] Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities

Tapolczai, K., Keck, F., Bouchez, A., Rimet, F., Kahlert, M., Vasselon, V. (2019). Frontiers in Ecology and Evolution, 7.

[14] The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Rimet, F., Abarca, N., Bouchez, A., Kusber, W.-H., Jahn, R., Kahlert, M., Keck, F., Kelly, M. G., Mann, D. G., Piuz, A., Trobajo, R., Tapolczai, K., Vasselon, V., Zimmermann, J. (2018). Fottea, 18(1), 37-54.

[13] River biofilm community changes related to pharmaceutical loads emitted by a wastewater treatment plant

Chonova, T., Labanowski, J., Cournoyer, B., Chardon, C., Keck, F., Laurent, É., Mondamert, L., Vasselon, V., Wiest, L., Bouchez, A. (2018). Environmental Science and Pollution Research, 25(10), 9254-9264.

[12] Disentangling the processes driving the biogeography of freshwater diatoms: A multiscale approach

Keck, F., Franc, A., Kahlert, M. (2018). Journal of Biogeography, 45(7), 1582-1592.

[11] Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

Keck, F., Vasselon, V., Rimet, F., Bouchez, A., Kahlert, M. (2018). Molecular Ecology Resources, 18(6), 1299-1309.

[10] Freshwater biomonitoring in the Information Age

Keck, F., Vasselon, V., Tapolczai, K., Rimet, F., Bouchez, A. (2017). Frontiers in Ecology and the Environment, 15(5), 266–274.

[9] Can we predict diatoms herbicide sensitivities with phylogeny? Influence of intraspecific and interspecific variability

Esteves, S. M., Keck, F., Almeida, S. F. P., Figueira, E., Bouchez, A., Rimet, F. (2017). Ecotoxicology, 26(8), 1065-1077.

[8] Phylogenetic signal in diatom ecology: Perspectives for aquatic ecosystems biomonitoring

Keck, F., Rimet, F., Franc, A., Bouchez, A. (2016). Ecological Applications, 26(3), 861–872.

[7] Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities

Chonova, T., Keck, F., Labanowski, J., Montuelle, B., Rimet, F., Bouchez, A. (2016). Science of The Total Environment, 542, 965-975.

[6] Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms

Keck, F., Bouchez, A., Franc, A., Rimet, F. (2016). Journal of Applied Ecology, 53(3), 856–864.

[5] phylosignal: an R package to measure, test, and explore the phylogenetic signal

Keck, F., Rimet, F., Bouchez, A., Franc, A. (2016). Ecology and Evolution, 6(9), 2774–2780.

[4] R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., Franc, A., Bouchez, A. (2016). Database, 2016, baw016.

[3] Linking Diatom Sensitivity to Herbicides to Phylogeny: A Step Forward for Biomonitoring?

Larras, F., Keck, F., Montuelle, B., Rimet, F., Bouchez, A. (2014). Environmental Science & Technology, 48(3), 1921-1930.

[2] Effects of Atmospheric Nitrogen Deposition on Remote Freshwater Ecosystems

Lepori, F., Keck, F. (2012). AMBIO: A Journal of the Human Environment, 41(3), 235-246.

[1] Can we predict nutrient limitation in streams and rivers?

Keck, F., Lepori, F. (2012). Freshwater Biology, 57(7), 1410–1421.

Software

R packages

refdb

A reference database manager for R

The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export reference genetic data. It has been designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in metabarcoding studies.

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bioseq

A toolbox for manipulating biological sequences in R

The purpose of bioseq is to provide a collection of classes and functions for biological sequence manipulation in R. The package provides simple S3 classes for sequences that are suitable for inclusion in a data frame and that can be analysed using the dplyr grammar and other tidyverse tools.

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diat.barcode

Access the diat.barcode database with R

The diatbarcode package provides an interface to download the database diat.barcode locally, in order to use it directly within the R environment. The diat.barcode database is a library of barcodes for diatoms and other algae which is curated by specialists and which guarantees good taxonomical homogeneity and good quality of sequences.

Go to GitHub
phylosignal

Exploring the phylogenetic signal in continuous traits

A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.

Go to GitHub
oviz

Maucha diagrams with R

Implementation of Maucha diagrams in R. See this blog post for more information.

Go to GitHub
rleafmap

Interactive maps with R and Leaflet

rleafmap is an R package to display spatial data with interactive maps powered by Leaflet. It is designed to be very easy to use and provides the features necessary to generate nice interactive maps with R.

Go to website