Publications

Articles

• Botella, C., Joly, A., Bonnet, P., Monestiez, P., & Munoz, F. (2018). Species distribution modeling based on the automated identification of citizen observations. Applications in Plant Sciences, 6(2), e1029. https://doi.org/10.1002/aps3.1029
• Botella, C., Joly, A., Monestiez, P., Bonnet, P., & Munoz, F. (2020) Bias in presence-only niche models related to sampling effort and species niches: Lessons for background point selection. PLOS ONE. https://doi.org/10.1371/journal.pone.0232078
• Botella, C., Joly, A., Bonnet, P., Munoz, F., & Monestiez, P. (2021). Jointly estimating spatial sampling effort and habitat suitability for multiple species from opportunistic presence-only data. Methods in Ecology and Evolution, 12(5), 933-945. https://doi.org/10.1111/2041-210X.13565 Download appendices
• Deneu, B., Servajean, M., Bonnet, P., Botella, C., Munoz, F., & Joly, A. (2021). Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment. PLoS computational biology, 17(4), e1008856. https://doi.org/10.1371/journal.pcbi.1008856
• Botella, C., Dray, S., Matias, C., Miele, V., & Thuiller, W. (2021). An appraisal of graph embeddings for comparing trophic network architectures. Methods in Ecology and Evolution, 13(1), 203-216. https://doi.org/10.1111/2041-210X.13738
• Gauzere, P., O Connor, L., Botella, C., Poggiato, G., Munkemuller, T., Pollock, L. J., ... & Thuiller, W. (2022). The diversity of biotic interactions complements functional and phylogenetic facets of biodiversity. Current Biology, 32(9), 2093-2100. https://doi.org/10.1016/j.cub.2022.03.009
• Botella, C., Bonnet, P., Hui, C., Joly, A., & Richardson, D. M. (2022). Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion. Biology, 11(9), 1293. https://doi.org/10.3390/biology11091293
• De Beer, I., Hui, C., Botella, C. & Richardson, D.M. (2023). Drivers of community turnover of narrow-ranged versus widespread naturalised woody plants in South Africa. Frontiers in Ecology And Evolution, 11, 103. https://doi.org/10.3389/fevo.2023.1106197
• Van der Colff, D., Kumschick, S., Foden, W., Raimondo, D., Botella, C., von Staden, L. & Wilson, J.R.U. (2023). Drivers, predictors, and probabilities of plant extinctions in South Africa. Biodiversity and Conservation. https://doi.org/10.1007/s10531-023-02696-7
• Botella, C., Gauzere, P., O'Connor, L., Ohlmann, M., Renaud, J., Dou, Y., Graham, C., Verburg, P., Maiorano, L., Thuiller, W. (2023). Land-use intensity influences European tetrapod food-webs. Ecology Letters (Under review).

Book chapters

• Botella, C., Joly, A., Bonnet, P., Monestiez, P., & Munoz, F. (2018). A Deep Learning Approach to Species Distribution Modelling. In Multimedia Tools and Applications for Environmental & Biodiversity Informatics (pp. 169-199). Springer, Cham. https://doi.org/10.1007/978-3-319-76445-0_10 Direct download.
• Joly, A., Goeau, H., Botella, C., Glotin, H., Bonnet, P., Vellinga, W.P., Planqué, R. & Muller, H. (2018). Overview of LifeCLEF 2018: A Large-Scale Evaluation of Species Identification and Recommendation Algorithms in the Era of AI: 9th International Conference of the CLEF Association, CLEF 2018, Avignon, France, September 10-14, 2018, Proceedings. https://doi.org/10.1007/978-3-319-98932-7_24
• Joly, A., Goeau, H., Botella, C., Kahl, S., Servajean, M., Glotin, H., ... & Muller, H. (2019, September). Overview of LifeCLEF 2019: identification of amazonian plants, South & North American birds, and niche prediction. In International Conference of the Cross-Language Evaluation Forum for European Languages (pp. 387-401). Springer, Cham. https://doi.org/10.1007/978-3-030-28577-7_29
• Deneu, B., Servajean, M., Botella, C., & Joly, A. (2019). Evaluation of deep species distribution models using environment and co-occurrences. In International Conference of the Cross-Language Evaluation Forum for European Languages (pp. 213-225). Springer, Cham.
• Joly, A., Goeau, H., Kahl, S., Deneu, B., Servajean, M., Cole, E., ... & Muller, H. (2020, September). Overview of LifeCLEF 2020: a system-oriented evaluation of automated species identification and species distribution Prediction. In International Conference of the Cross-Language Evaluation Forum for European Languages (pp. 342-363). Springer, Cham. https://doi.org/10.1007/978-3-030-58219-7_23
• Botella, C., Marchante, H., Celesti-Grapow, L., Brundu, G., Geerts, S., Ramirez-Albores, J., Gonzalez-Moreno, P., Ritter, M. & Richardson, D.M. (2023) The global distribution of Acacia. In Wattles – Australian Acacia species around the world. CABI. https://doi.org/10.1079/9781800622197.0009

Datasets

• Cole, E., Deneu, B., Lorieul, T., Servajean, M., Botella, C., Morris, D., ... & Joly, A. (2020). The geolifeclef 2020 dataset. arXiv preprint https://doi.org/10.48550/arXiv.2004.04192
• Botella, C., Deneu, B., Marcos, D., Servajean, M., Estopinan, J., Larcher, T., ... & Joly, A. (2023). The GeoLifeCLEF 2023 Dataset to evaluate plant species distribution models at high spatial resolution across Europe. arXiv preprint. https://doi.org/10.48550/arXiv.2308.05121

Scientific outreach

• Castagneyrol, B., Botella, C. & Fontaine, B. (2022). Sciences citoyennes et qualité des données sur la biodiversité: Un faux problème? Numéro spécial #1, art. 6. Novae, INRAE. https://doi.org/10.17180/novae-2022-ns01-art06
• Streito, J. C., Papaix, J., Chartois, M., Botella, C., Pierre, E., Armand, J. M., ... & Rossi, J. P. (2023). Les citoyens, sentinelles de la surveillance phytosanitaire?. In Crises sanitaires en agriculture: Les espèces invasives sous surveillance (pp. 151-166). Quae. Link

Working notes

• Botella, C., Bonnet, P., Munoz, F., Monestiez, P., & Joly, A. (2018, September). Overview of GeoLifeCLEF 2018: location-based species recommendation. In CLEF 2018. Download pdf.
• Deneu, B., Servajean, M., Botella, C., & Joly, A. (2018, September). Location-based species recommendation using co-occurrences and environment-GeoLifeCLEF 2018 challenge. In CLEF 2018. Download pdf.
• Botella, C., Servajean, M., Bonnet, P., & Joly, A. (2019, September). Overview of GeoLifeCLEF 2019: plant species prediction using environment and animal occurrences. In Working Notes of CLEF 2019-Conference and Labs of the Evaluation Forum (No. 2380). HAL Link
• Deneu, B., Lorieul, T., Cole, E., Servajean, M., Botella, C., Bonnet, P., & Joly, A. (2020). Overview of LifeCLEF location-based species prediction task 2020 (GeoLifeCLEF). CEUR-WS. Agritrop Link
• Botella, C., Deneu, B., Gonzalez, D. M., Servajean, M., Larcher, T., Leblanc, C., ... & Joly, A. (2023). Overview of GeoLifeCLEF 2023: Species Composition Prediction with High Spatial Resolution at Continental Scale Using Remote Sensing. In Working Notes of CLEF 2023-Conference and Labs of the Evaluation Forum. temporary_link

Updated on 1st september 2023.