papers
We strive to make all our science publicly available and open in bioRxiv, other preprint media, or in our website (feel free to reach out for any reprint or google sci-hub)
Trainees in our lab are free to lead their own independent ideas or collaborative work, so Moi may not necessarily be part of some papers. Check out the Google Scholar page from Moi here and for team members on the team page.
2024
Global coral genomic vulnerability explains recent reef losses
Selmoni, O., Cleves, P.C., Exposito-Alonso, M.,
bioRxiv (2024) https://doi.org/10.1101/2023.10.16.562583 [pdf]
Finding genes and pathways that underlie coral adaptation
Selmoni, O., Bay. L.K., Exposito-Alonso, M., Cleves, P.C.
Trends in Genetics (2024) https://doi.org/10.1016/j.tig.2024.01.003 [pdf]
2023
An encyclopedia of enhancer-gene regulatory interactions in the human genome.
Gschwind, A. R., K. S. Mualim, A. Karbalayghareh, M. U. Sheth, K. K. Dey, E. Jagoda, R. N. Nurtdinov, W. Xi, A. S. Tan, H. Jones, X. Rosa Ma, D. Yao, J. Nasser, Z. Avsec, B. T. James, M. S. Shamim, N. C. Durand, S. S. P. Rao, R. Mahajan, B. R. Doughty, K. Andreeva, J. C. Ulirsch, K. Fan, E. M. Perez, T. C. Nguyen, D. R. Kelley, H. K. Finucane, J. E. Moore, Z. Weng, M. Kellis, M. C. Bassik, A. L. Price, M. A. Beer, R. Guigo, J. A. Stamatoyannopoulos, E. L. Aiden, W. J. Greenleaf, C. S. Leslie, L. M. Steinmetz, A. Kundaje, and J. M. Engreitz
bioRxiv (2023), https://doi.org/10.1101/2023.11.09.563812
Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana
Megan Ruffley, Laura Leventhal, Shannon Hateley, Seung Y. Rhee, Moises Exposito-Alonso
bioRxiv (2023) https://doi.org/10.1101/2023.10.16.562583 [pdf]
grenedalf: population genetic statistics for the next generation of pool sequencing
Lucas Czech, Jeffrey P. Spence, Moises Exposito-Alonso
arXiv (2023), https://arxiv.org/abs/2306.11622 [pdf]
Climate lags and genetics determine phenology in quaking aspen (Populus tremuloides)
Blonder, Benjamin W; Brodrick, Philip G; Chadwick, K Dana; Carroll, Erin; Cruz-de Hoyos, Roxanne M; Expósito-Alonso, Moisés; Hateley, Shannon; Moon, Minkyu; Ray, Courtenay A; Tran, Hoang; Walton, James A
New Phytologist (2023) https://doi.org/10.1111/nph.18850 [pdf]
The Reef Environment Centralized InFormation System (RECIFS) : An integrated geo‐environmental database for coral reef research and conservation
Oliver Selmoni, Gael Lecellier, Veronique Berteaux-Lecellier, and Stephane Joost.
Global Ecology & Biogeography (2023), http://dx.doi.org/10.1111/geb.13657 [pdf]
Understanding local plant extinctions before it’s too late: bridging evolutionary genomics with global ecology.
Exposito-Alonso, M.
New Phytologist (2022), https://doi.org/10.1111/nph.18718 (Tansley Medal) [pdf]
Featuring article in New Phytologist
https://doi.org/10.1111/nph.18735
An image is worth a thousand species: combining neural networks, citizen science, and remote sensing to map biodiversity
Gillespie, Lauren, Ruffley, Megan; Exposito-Alonso, Moises.
bioRxiv (2023). https://doi.org/10.1101/2022.08.16.504150 [pdf]
2022
Towards a genetic theory of island biogeography: Inferring processes from multidimensional community-scale data
Isaac Overcast, Guillaume Achaz, Robin Aguilée, Carmelo Andújar, Paula Arribas, Thomas J. Creedy, Evan P. Economo, Rampal S. Etienne, Rosemary Gillespie, Claire Jacquet, Flora Jay, Susan Kennedy, Henrik Krehenwinkel, Amaury Lambert, Emmanouil Meramveliotakis, Víctor Noguerales, Benoit Perez-Lamarque, George Roderick, Haldre Rogers, Megan Ruffley, Isabel Sanmartin, Alfried P. Vogler, Anna Papadopoulou, Brent C. Emerson, Hélène Morlon .
Global Ecology and Biogeography (2022), https://doi.org/10.1111/geb.13604 [pdf]
Power and limitations of the mutations-area relationship to assess within-species genetic diversity targets for post-2020 Sustainable Development Goals
Exposito-Alonso et al.
EcoEvoRxiv (2022) https://doi.org/10.32942/X2F30P [pdf]
Wide-ranging consequences of priority effects governed by an overarching factor
Chappell, C. R., M. K. Dhami, M. C. Bitter, L. Czech, S. Herrera Paredes, F. B. Barrie, Y. Calderón, K. Eritano, L.-A. Golden, D. Hekmat-Scafe, V. Hsu, C. Kieschnick, S. Malladi, N. Rush, and T. Fukami.
eLife (2022), http://dx.doi.org/10.7554/eLife.79647 [pdf]
Century-long timelines of herbarium genomes predict plant stomatal response to climate change
Lang, Patricia L M; Erberich, Joel M; Lopez, Lua; Weiss, Clemens L; Amador, Gabriel; Fung, Hannah F; Latorre, Sergio M; Lasky, Jesse R; Burbano, Hernan A; Exposito-Alonso, Moises; Bergmann, Dominique
bioRxiv (2022) http://dx.doi.org/10.1101/2022.10.23.513440 [pdf]
A reference genome assembly of the bobcat, Lynx rufus.
Lin, M., M. Escalona, R. Sahasrabudhe, O. Nguyen, E. Beraut, M. R. Buchalski, and R. K. Wayne. (2022).
Journal of Heredity (2022) doi: 10.1093/jhered/esac031. [pdf]
A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad (Bombina orientalis) in Beijing.
Zhang, S., M. Lin, J. Liu, J. Chen, D. Liu, J. Zhao, and M. Yao.
BMC Ecology & Evolution (2022) doi: 10.1186/s12862-022-02072-z [pdf]
Genetic diversity loss in the Anthropocene
Exposito-Alonso, M., Booker, T. A., Czech, L., Gillespie, L., Hateley, S., Kyriazis, C. C., Lang, P. Leventhal, L. Nogues-Bravo, D., Pagowski, V. Ruffley, M., Spence, J. P., Toro Arana, S., Weiss, C. and Zess, Erin.
Science https://doi.org/10.1126/science.abn5642 [pdf]
Media coverage in English
Twitter TLDR -> https://twitter.com/MExpositoAlonso/status/1573038681359003648
Interview at The Scientist "Are We In the Midst of a Silent Mass Extinction?"
Noticias en Español
Article in La Vanguardia "El Antropoceno ha provocado ya la destrucción de más del 10% de la diversidad genética del planeta"
Interview in El Pais "El Antropoceno ya ha provocado una pérdida de Biodiversidad irreparable"
Entrevista en Radiotelevisión Española RTVE "Cómo conseguir que las plantas resistan al cambio climático"
grenepipe: A flexible, scalable, and reproducible pipeline to automate variant and frequency calling from sequence reads
Czech, L., Exposito-Alonso, M.
Bioinformatics (2022) https://doi.org/10.1093/bioinformatics/btac600 [pdf]
Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform
LaRue T, Lindner H, Srinivas A, Exposito-Alonso M, Lobet GR, Dinneny JR.
eLife (2022) https://doi.org/10.7554/eLife.76968. bioRxiv (2021). https://doi.org/10.1101/2021.11.13.468476
From Coral Reefs to Joshua Trees: What Ecological Interactions Teach Us about the Adaptive Capacity of Biodiversity in the Anthropocene
Lagerstrom, Katherine M., Summer Vance, Brendan H. Cornwell, Megan Ruffley, Tatiana Bellagio, Moi Exposito-Alonso, Stephen R. Palumbi, and Elizabeth A. Hadly. 2022
Philosophical Transactions of the Royal Society of London. Series B . http://dx.doi.org/10.1101/2022.02.02.477408
Genomic Evidence of an Ancient Inland Temperate Rainforest in the Pacific Northwest of North America
Megan Ruffley, Megan L. Smith, Anahí Espíndola, Daniel F. Turck, Niels Mitchell, Bryan Carstens, Jack Sullivan, David C. Tank
Molecular Ecology (2022). https://doi.org/10.1111/mec.16431.
Metagenomic Analysis Using Phylogenetic Placement -- A Review of the First Decade.
Czech, Lucas, Alexandros Stamatakis, Micah Dunthorn, and Pierre Barbera.
arXiv (2022). http://arxiv.org/abs/2202.03534
Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana?
Estarague, A., Vasseur, F., Sartori, K., Bastias, C., Cornet, D., Rouan, L., Beurier, G., Exposito-Alonso, M., Herbette, S., Bresson ,J., Vile, D., and Violle, C.
Annals of Botany (2022). https://doi.org/10.1093/aob/mcab149.
Monitoring rapid evolution of plant populations at scale with Pool-Sequencing
Czech, Lucas; Peng, Yunru; Spence, Jeffrey P; Lang, Patricia L M; Bellagio, Tatiana; Hildebrandt, Julia; Fritschi, Katrin; Schwab, Rebecca; Rowan, Beth A; GrENE-net consortium; Weigel, Detlef; Scheepens, J F; Vasseur, François; Exposito-Alonso, Moises. 2022
bioRxiv. http://dx.doi.org/10.1101/2022.02.02.477408 [pdf]
Mutation bias reflects natural selection in Arabidopsis thaliana
Monroe, J Grey; Srikant, Thanvi; Carbonell-Bejerano, Pablo; Becker, Claude; Lensink, Mariele; Exposito-Alonso, Moises; Klein, Marie; Hildebrandt, Julia; Neumann, Manuela; Kliebenstein, Daniel; Weng, Mao-Lun; Imbert, Eric; Ågren, Jon; Rutter, Matthew T; Fenster, Charles B; Weigel, Detlef. 2022
Nature. https://doi.org/10.1101/2020.06.17.156752 [pdf]
The scientist: https://www.the-scientist.com/news-opinion/essential-genes-protected-from-mutations-69643
Plantae Highlight: https://buff.ly/38u0xDl
Company of Biologists Highlight: https://doi.org/10.1242/prelights.22698
2021
Haldane's cost of selection imposes a mild constraint on adaptation, with a high proportion of deaths in A. thaliana being selective
Metheson, J., Exposito-Alonso M., Masel, J.
bioRxiv (2021) https://www.biorxiv.org/content/10.1101/2021.10.13.464000v1 [pdf]
The history and geographic distribution of a KCNQ1 atrial fibrillation risk allele
Hateley S, Lopez-Izquierdo A, Jou CJ, Cho S, Schraiber JG, Song S
Nature Communications (2021) 12: 1–10. https://doi.org/10.1038/s41467-021-26741-7 [pdf]
Vision, Challenges and Opportunities for a Plant Cell Atlas
Plant Cell Atlas Consortium, Suryatapa Ghosh Jha, Alexander T. Borowsky, Benjamin J. Cole, Noah Fahlgren, Andrew Farmer, Shao-Shan Carol Huang, et al. 2021.
eLife (2021): e66877. https://doi.org/10.7554/eLife.66877. [pdf]
How will mosquitoes adapt to climate change?
Couper, L., Farner, J., Caldwell, J., Childs, M., Harris, M., Kirk, D., Nova, N., Shocket, M., Skinner, E., Uricchio, L., Exposito-Alonso, M., Mordecai, E.,.
eLife (2021): e69630. https://doi.org/10.7554/eLife.69630 [pdf]
CRISPR-Cas9 and beyond: What’s next in Plant Genome Engineering
Zess, E., and Matthew B.
Vitro Cellular & Developmental Biology - Plant (2021) [pdf]
A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
Dorone, Y., Boeynaems, S., Flores, E.; Jin, B. Hateley, S., Bossi, F., Elena L., Pennington J.G.; Michiels, E., De Decker, M., Vints, K., Baatsen, P., Bassel, G.W., Otegui, M.S., Holehouse, A.S., Exposito-Alonso, M., Sukenik, S., Gitler, A.D., Rhee, S.Y.
Cell (2021) http://dx.doi.org/10.1016/j.cell.2021.06.009 [pdf]
Carnegie PR highlight: https://carnegiescience.edu/news/how-seeds-know-its-good-time-germinate
grenepipe: A flexible, scalable, and reproducible pipeline to automate variant and frequency calling from sequence reads
Czech, L., Exposito-Alonso, M.
arXiv (2021) https://arxiv.org/abs/2103.15167 [pdf]
Prospects and limitations of genomic offset in conservation management
Rellstab, C., Dauphin, B., Exposito‐Alonso, M.,
Evolutionary Applications (2021) 14:1202–1212. [pdf]
Small Peptides Modulate the Immune Function of the Ion Channel-like Protein ACD6 in Arabidopsis thaliana
Zhu, W., Li, L., Neuhaeuser, B., Thelen, M., Wang, M., Chen, J., Wei, L., Venkataramani, K., Exposito-Alonso, M., Liu, C., Keck, J., Barragan, A. C., Schwab, R., Lutz, U., Ludewig, U., Weigel, D..
bioRxiv (2021). https://doi.org/10.1101/2021.01.25.428077. [pdf]
The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils.
Gottschling, Marc, Lucas Czech, Frédéric Mahé, Sina Adl, and Micah Dunthorn.
The Journal of Eukaryotic Microbiology 68 (1): e12833. https://doi.org/10.1111/jeu.12833.
2020
Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.
Morel, Benoit, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukas Hübner, Sarah Lutteropp, Dora Serdari, et al..
Molecular Biology and Evolution (2021) : Volume 38, Issue 5, May 2021, Pages 1777–1791, https://doi.org/10.1093/molbev/msaa314
Using Taxonomically-Informed Convolutional Neural Networks To Predict Plant Biodiversity Across California From High-Resolution Satellite Imagery Data.
Gillespie, L & Exposito-Alonso, M.
AGU Fall Meeting (2020). https://agu.confex.com/agu/fm20/webprogram/Paper712115.html.
Genomic Prediction of (Mal)Adaptation across Current and Future Climatic Landscapes.
Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, and Keller S R.
Annual Reviews of Ecology, Evolution, and Systematics (2020) 51 (1): 245–69. https://doi.org/10.1146/annurev-ecolsys-020720-042553 [pdf]
Current status of the multinational Arabidopsis community.
Geraint Parry, Nicholas J. Provart , Siobhan M. Brady, Baris Uzilday, The Multinational Arabidopsis Steering Committee.
Plant Direct, https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.248 [pdf]
Non-additive polygenic models improve predictions of fitness traits in three eukaryote model species.
Exposito-Alonso M, Wilton P, Nielsen R. 2020.
bioRxiv. https://doi.org/10.1101/2020.07.14.194407[pdf]
Seasonal timing adaptation across the geographic range of Arabidopsis thaliana.
Exposito-Alonso M. (2020).
PNAS, 117 (18) 9665-9667 [pdf]
Evolutionary genomics improves prediction of species responses to climate change.
Waldvogel AM, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. (2020)
Evolution Letters, https://doi.org/10.1002/evl3.154 [pdf]
2019
The Earth BioGenome project: Opportunities and Challenges for Plant Genomics and Conservation
Exposito-Alonso, M., Drost, HG., Burbano, H.A., Weigel, D. (2019)
The Plant Journal, https://doi.org/10.1111/tpj.14631 [pdf]
Natural selection on the Arabidopsis thaliana genome in present and future climates.
Exposito-Alonso, M., 500 Genomes Field Experiment Team, Burbano, H. A., Bossdorf, O., Nielsen, R., Weigel, D.
Nature (2019), https://doi.org/10.1038/s41586-019-1520-9 [pdf]
Highlights: Surridge C. Genomic futurology. Nat Plants. 2019;5: 1027. doi:10.1038/s41477-019-0532-7
A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions.
Exposito-Alonso, M., Rodríguez, R.G., Barragán, C., Capovilla, G., Chae, E., Devos, J., Dogan, E.S., Friedemann, C., Gross, C., Lang, P., Lundberg, D., Middendorf, V., Kageyama, J., Karasov, T., Kersten, S., Petersen, S., Rabbani, L., Regalado, J., Reinelt, L., Rowan, B., Seymour, D.K., Symeonidi, E., Schwab, R., Tran, D.T.N., Venkataramani, K., Van de Weyer, A.-L., Vasseur, F., Wang, G., Wedegärtner, R. Weiss, F., Wu, R., Xi, W., Zaidem, M., Zhu, W., García-Arenal, F., Burbano, H.A., Bossdorf, O., Weigel, D.,
bioRxiv (final version) (2019), https://doi.org/10.1101/186767. [pdf]
pre-2018
Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana.
Exposito-Alonso, M., Brennan, A., Alonso-Blanco, C., Picó, F.X., (2018)
Evolution, 71:550. https://doi.org/10.1111/evo.13508. [pdf]
Adaptive diversification of growth allometry in the plant Arabidopsis thaliana
Vasseur, F., Exposito-Alonso, M., Ayala-Garay, O., Wang, G., Enquist, B.J., Violle, C., Ville, D., Weigel, D., (2018)
PNAS, https://doi.org/10.1073/pnas.1709141115 [pdf]
The rate and effect of new mutations in a colonizing plant lineage.
Exposito-Alonso, M.*, Becker, C*., Schuenemann, V.J., Reitter, E., Setzer, C., Slovak, R., Brachi, B., Hagmann, J., Grimm, D.G., Jiahui, C., Busch, W., Bergelson, J., Ness, R.W., Krause, J., Burbano, H.A., Weigel, D., (2018)
PLOS Genetics, 14, e1007155. https://doi.org/10.1371/journal.pgen.1007155 [pdf]
Cover highlight > http://blogs.plos.org/biologue/files/2018/02/Feb_2018.pdf
Max Planck Highlight: Evolutionwatch for plants > https://www.mpg.de/11956930/evolutionwatch-plants
Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana.
Exposito-Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H.A., Weigel, D., (2018).
Nature Ecology & Evolution 2, 352–358. https://doi.org/10.1038/s41559-017-0423-0 [pdf]
Max Planck Highlight: Life on the edge > https://www.mpg.de/11861946/arabidopsis-climate-change
Behind the paper > https://natureecoevocommunity.nature.com/users/77335-moises-exposito-alonso/posts/28790-life-on-the-edge-prepares-plants-for-climate-change
On the post-glacial spread of human commensal Arabidopsis thaliana.
Lee, C.-R., Svardal, H., Farlow, A., Exposito-Alonso, M., Ding, W., Novikova, P., Alonso-Blanco, C., Weigel, D., Nordborg, M., (2017).
Nature Communications. 8, 14458. https://doi.org/10.1038/ncomms14458. [pdf]
World Scientists’ Warning to Humanity: A Second Notice.
[Signatory] Ripple, William J., Christopher Wolf, Thomas M. Newsome, Mauro Galetti, Mohammed Alamgir, Eileen Crist, Mahmoud I. Mahmoud, and William F. Laurance.
Bioscience (2017), November. https://doi.org/10.1093/biosci/bix125.
Epigenomic diversity in a global collection of Arabidopsis thaliana accessions.
Kawakatsu, T., Huang, S. C., Jupe, F., Sasaki, E., Schmitz, R. J., Urich, M. A., Castanon, R., Nery, J. R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C. R., Wang, C., Bemm, F., Becker, C., O'Neil, R., O'Malley, R. C., Quarless, D. X., 1001 Genomes Consortium, Schork, N. J., Weigel, D., Nordborg, M., Ecker, J. R.
Cell (2016) 166, 492-505, doi.org/10.1016/j.cell.2016.06.044. [pdf]
Effector-triggered immune response in Arabidopsis thaliana is a quantitative trait.
Iakovidis, M., Teixeira, P.J.P.L., Exposito-Alonso, M., Cowper, M.G., Law, T.F., Liu, Q., Vu, M.C., Dang, T.M., Corwin, J.A., Weigel, D., Dangl, J.L., Grant, S.R.,.
Genetics (2016) 204, 337–353. https://doi.org/10.1534/genetics.116.190678. [pdf]
1,135 Genomes reveal the global pattern of polymorphism in Arabidopsis thaliana.
1001 Genomes Consortium
Cell (2016) 166, 481–491. https://doi.org/10.1016/j.cell.2016.05.063. [pdf]