papers



For team member's Google Scholars see team page

2022


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
Czech, Lucas, Alexandros Stamatakis, Micah Dunthorn, and Pierre Barbera.
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]

Genetic diversity loss in the Anthropocene
Exposito-Alonso , M., Booker, T. A., Czech, L., Fukami, T., 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.
bioRxiv (2021) https://doi.org/10.1101/2021.10.13.464000 [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]

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.
bioRxiv (2021). https://doi.org/10.1101/2021.11.13.468476

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]