Peer-reviewed Articles
2024
11- Allio, R., Delsuc, F., Belkhir, K., Douzery, E. J., Ranwez, V., & Scornavacca, C. (2024). OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics. Nucleic Acids Research, 52(D1), D529-D535. DOI: 10.1093/nar/gkad834
2023
10- Haran, J.*, Li, X.*, Allio, R.*, Shin, S., Benoit, L., Oberprieler, R. G., Farell, B. D., Brown, S. D. J., Leschen, R. A. B., Kergoat, G. J. & McKenna, D. D. (2023). Phylogenomics illuminates the phylogeny of flower weevils (Curculioninae) and reveals ten independent origins of brood-site pollination mutualism in true weevils. Proceedings of the Royal Society B, 290(2008), 20230889. DOI: 10.1098/rspb.2023.0889
9- Heighton, S. P.*, Allio, R.*, Murienne, J., Salmona, J., Meng, H., Scornavacca, C., Bastos, A.D.S., Njiokou, F., Pieterson, D.W., Tilak, M.-K., Luo, S.-J., Delsuc, F., & Gaubert, P. (2023). Pangolin genomes offer key insights and resources for the world’s most trafficked wild mammals. Molecular Biology and Evolution, Volume 40, Issue 10, October 2023, msad190. DOI: 10.1093/molbev/msad190
8- Comte, A., Tricou, T., Tannier, E., Joseph, J., Siberchicot, A., Penel, S., Allio, R., Delsuc, F., Dray, S., & de Vienne, D. M. (2023). PhylteR: efficient identification of outlier sequences in phylogenomic datasets. Molecular Biology and Evolution, Volume 40, Issue 11, November 2023, msad234. DOI: 10.1093/molbev/msad234
7- Coiro, M., Allio, R., Mazet, N., Seyfullah, L. J., & Condamine, F. L. (2023). Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity. New Phytologist. DOI: 10.1111/nph.19010
6- Condamine, F. L., Allio, R., Reboud, E. L., Dupuis, J. R., Toussaint, E. F., Mazet, N., Hu S.-J., Lewis D.S., Kunte K., Cotton A. M., & Sperling, F. A. (2023). A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae). Molecular Phylogenetics and Evolution, 183, 107758. DOI: 10.1016/j.ympev.2023.107758
2021
5- Allio R., Tilak M. K., Scornavacca C., Avenant N. L., Corre E., Nabholz B., & Delsuc F. (2021). High-quality carnivore genomes from roadkill samples enable species delimitation in aardwolf and bat-eared fox. eLife, 10, e63167. DOI: 10.7554/eLife.63167
2020
4- Allio R., Nabholz B., Wanke S., Chomicki G., Pérez-Escobar O. A., Cotton A. M., Clamens A.- L., Kergoat G. J., Sperling F. A. H. & Condamine F. L. (2020). Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nature communications, 12(1), 354. DOI: 10.1038/s41467-020-20507-3
3- Allio, R., Schomaker‐Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020). MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Molecular Ecology Resources, 20(4), 892-905. DOI: 10.1111/1755-0998.13160
2- Allio, R., Scornavacca, C., Nabholz, B., Clamens, A. L., Sperling, F. A., & Condamine, F. L. (2020). Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution. Systematic Biology, 69(1), 38-60. DOI: 10.1093/sysbio/syz030
2017
1- Allio, R., Donega, S., Galtier, N., & Nabholz, B. (2017). Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker. Molecular biology and evolution, 34(11), 2762-2772. DOI: 10.1093/molbev/msx197
Preprints
4- Battlay, P., Hendrickson, B. T., Mendez-Reneau, J. I., Santangelo, J. S., Albano, L. J., Wilson, J., Caizergues, A., [9 authors], Allio, R., [35 authors] & Kooyers, N. J. (2024). Structural variants underlie parallel adaptation following global invasion. bioRxiv, 2024-07. DOI: 10.1101/2024.07.09.602765
3- Perrier, C., Allio, R., Legeai, F., Gautier, M., Beneluz, F., Marande, W., Theron, A., Rodde, N., Herrera, M., Saune, L. and Parrinello, H. (2024). Transposable element accumulation drives genome size increase in Hylesia metabus (Lepidoptera: Saturniidae), an urticating moth species from South America. bioRxiv, 2024-07. DOI: 10.1101/2024.07.11.602864
2- Zelvelder, B., Kergoat, G. J., Benoit, L., Tsuchida, T., Haran, J., & Allio, R. (2024). The first example of extreme and independent host plant shifts mediated by parasitic plants in insects. bioRxiv, 2024-04. DOI: 10.1101/2024.04.03.587887
1- Allio, R., Teullet, S., Lutgen, D., Magdeleine, A., Koual, R., Tilak, M. K., de Thoisy, B., Emerling, C.A., Lefebure, T., & Delsuc, F. (2022). Comparative transcriptomics reveals divergent paths of chitinase evolution underlying dietary convergence in ant-eating mammals. bioRxiv, 2022-11. DOI: 10.1101/2022.11.29.518312