Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses
- 1Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA 14853
Abstract
Grasses (Poaceae) dominate terrestrial ecosystems and sustain global food security, yet the genomic principles enabling their repeated adaptation to extreme environments remain unresolved. Combining dense phylogenomic sampling, global environmental data, and genomic large language models (gLLMs), we characterize the mutational targets underlying environmental shift across 687 genomes from 561 species spanning 17 climate zones. We identify 17-30 phylogenetically independent transitions into extreme temperature, water, and soil environments, accompanied by convergent shifts in genome-scale molecular properties, including the Nitrogen-to-Carbon balance and the biosynthetic cost of the proteome. Our gLLMs-informed phylogenetic mixed modeling framework identifies 330 genes that repeatedly associated with distinct axes of environmental variation, highlighting the importance of protein modification and localization within extracellular and organellar compartments. Overlaying independent convergent selection tests identifies 27 high-confidence candidates for further characterization. Together, our results show that grass adaptation is canalized by layered constraints at genome-wide and gene-specific scales, producing predictable evolutionary trajectories.
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BibTeX
@misc{hsu2026convergent,
title = {{Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses}},
author = {S.-K. Hsu and A. J. Schulz and C. O. Hale and G. Costa-Neto and Z. R. Miller and M. C. Stitzer and T. Wrightsman and J. Zhai and W.-Y. Lai and H. D. Dawson and Q. Wang and T. M. AuBuchon-Elder and L. J. Brindisi and E. Oren and Y. Luo and B. A. Konadu and J. O. Ojeda-Rivera and M. Pennell and E. A. Kellogg and M. C. Romay and E. S. Buckler},
howpublished = {bioRxiv},
year = {2026},
month = jun,
doi = {10.64898/2026.06.01.729361},
url = {https://www.biorxiv.org/content/10.64898/2026.06.01.729361v3},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses
AU - S.-K. Hsu
AU - A. J. Schulz
AU - C. O. Hale
AU - G. Costa-Neto
AU - Z. R. Miller
AU - M. C. Stitzer
AU - T. Wrightsman
AU - J. Zhai
AU - W.-Y. Lai
AU - H. D. Dawson
AU - Q. Wang
AU - T. M. AuBuchon-Elder
AU - L. J. Brindisi
AU - E. Oren
AU - Y. Luo
AU - B. A. Konadu
AU - J. O. Ojeda-Rivera
AU - M. Pennell
AU - E. A. Kellogg
AU - M. C. Romay
AU - E. S. Buckler
PY - 2026
DA - 2026/06/01
PB - bioRxiv
DO - 10.64898/2026.06.01.729361
UR - https://www.biorxiv.org/content/10.64898/2026.06.01.729361v3
AB - Grasses (Poaceae) dominate terrestrial ecosystems and sustain global food security, yet the genomic principles enabling their repeated adaptation to extreme environments remain unresolved. Combining dense phylogenomic sampling, global environmental data, and genomic large language models (gLLMs), we characterize the mutational targets underlying environmental shift across 687 genomes from 561 species spanning 17 climate zones. We identify 17-30 phylogenetically independent transitions into extreme temperature, water, and soil environments, accompanied by convergent shifts in genome-scale molecular properties, including the Nitrogen-to-Carbon balance and the biosynthetic cost of the proteome. Our gLLMs-informed phylogenetic mixed modeling framework identifies 330 genes that repeatedly associated with distinct axes of environmental variation, highlighting the importance of protein modification and localization within extracellular and organellar compartments. Overlaying independent convergent selection tests identifies 27 high-confidence candidates for further characterization. Together, our results show that grass adaptation is canalized by layered constraints at genome-wide and gene-specific scales, producing predictable evolutionary trajectories.
ER -