Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Wenjie Mu, Kexin Li, Yongzhi Yang, Adina Breiman, Shangling Lou, Jiao Yang, Ying Wu, Shuang Wu, Jianquan Liu, Eviatar Nevo, Pilar Catalan

Research output: Contribution to journalArticlepeer-review


Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains a captivating topic in evolutionary biology. However, the pattern of genetic divergence underlying this process across the genome may vary between species and mating systems. Here, we present evidence that Brachypodium stacei, an annual and highly selfing grass model species, has undergone sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses together with lab experiments mimicking the two opposite environmental conditions suggest that diploid B. stacei populations have diverged sympatrically in two slopes characterized by distinct biomes at Evolution Canyon I (ECI), Mount Carmel, Israel. Despite ongoing gene flow, primarily facilitated by seed dispersal, the level of gene flow has progressively decreased over time. This local adaptation involves the scattered divergence of many unlinked loci across the total genome that include both coding genes and noncoding regions. Additionally, we have identified significant differential expressions of genes related to the ABA signaling pathway and contrasting metabolome composition between the arid- vs. forest-adapted B. stacei populations in ECI. These results suggest that multiple small loci involved in environmental responses act additively to account for ecological adaptations by this selfing species in contrasting environments.

Original languageEnglish
Article numbere2304848120
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number45
StatePublished - 7 Nov 2023

Bibliographical note

Publisher Copyright:
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  • Brachypodium stacei
  • ecological divergence
  • functional genomics
  • multiomics
  • selfing species

ASJC Scopus subject areas

  • General


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