Genome structures

The role of structural variation in speciation and adaptation

Single nucleotide polymorphism (SNP) datasets can be used to dissect the genomic basis of fitness-relevant traits, but this is only one component of adaptive genetic variation. Structural rearrangements (structural variants, or SVs) can impact gene function and the content and structure of chromosomes, representing remarkable sources of functional genomic variation. Yet our understanding of the role of structural rearrangements in species diversification and adaptation to environmental change is still challenged by most sequencing methods. We use novel sequencing and computational techniques to study structural variation at a population scale.

Representative publications on this topic include:

  1. Joana L. Rocha, Runyang Nicolas Lou, Carolina L. De Lima Adam, et al. (2026). A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos. bioRxiv (preprint). 10.64898/2026.06.06.730619
  2. Joana L. Rocha*, Runyang Nicolas Lou*, and Peter H. Sudmant (2024). Structural variation in humans and our primate kin in the era of T2T genomes and pangenomics. Current Opinion in Genetics & Development. 10.1016/j.gde.2024.102233
    *co-first authors
  3. Davide Bolognini*, Alma Halgren*, Runyang Nicolas Lou*, Alessandro Raveane*, Joana L. Rocha*, et al. (2024). Recurrent evolution and selection shape structural diversity at the amylase locus. Nature. 10.1038/s41586-024-07911-1
    *co-first authors
  4. Joana L. Rocha, Pedro Silva, Nuno Santos, et al. (2023). North-African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nature Ecology & Evolution. 10.1038/s41559-023-02094-w

Media highlights:

  1. Humans have evolved to digest starch more easily since the advent of farming — Nature Research Briefing, by Joana L. Rocha and Runyang N. Lou
  2. Agriculture accelerated human genome evolution to capture energy from starchy foods — UC Berkeley News, by Robert Sanders