genome structures

The role of structural variation in speciation and adaptation

Though single nucleotide polymorphism (SNP) datasets can be used to dissect the genomic basis of fitness-relevant traits, this is only one component of adaptive genetic variation. Structural rearrangements (structural variation or SVs), for instance, can impact gene function and the content and structure of chromosomes, thus representing remarkable sources of functional genomic variation. However, our understanding of the role of structural rearrangements within a genome on species diversification and adaptation to environmental change is still challenged by most sequencing methods. During my postdoctoral research I have been using 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 *, Peter H Sudmant (2024): Structural variation in humans and our primate kin in the era of T2T genomes and pangenomics (Current Opinion in Genetics and Development, DOI: https://doi.org/10.1016/j.gde.2024.102233) *denotes co-first author
  2. 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, DOI:https://doi.org/10.1038/s41586-024-07911-1) *denotes co-first author
  3. Joana L. Rocha, Pedro Silva, Nuno Santos, Monia Nakamura, Sandra Afonso, Abdeljebbar Qninba, Zbyszek Boratynski, Peter H. Sudmant, Jose C. Brito, Rasmus Nielsen‡ and Raquel Godinho‡ (2023), North-African fox genomes show signatures of repeated introgression and adaptation to life in deserts (Nature Ecology and Evolution; DOI: https://doi.org/10.1038/s41559-023-02094-w).

Media highlights on this topic:

  1. Humans have evolved to digest starch more easily since the advent of farming, written by me and Nicolas for Nature Research Briefing

  2. Agriculture accelerated human genome evolution to capture energy from starchy foods, written by Robert Sanders for Science and Environment Research section of UC Berkeley News, Online issue September 4, 2024

When humans domesticated grains some 12,000 years ago, natural selection began to favor genomes with extra genes encoding for the enzyme amylase, which converts starch to sugar. These extra genes slipped into the same region of the genome where the three amylase genes originally sat (top set of arrows), though some became reversed (lower sets of arrows). Multiple copies of amylase genes presumably allowed agrarian societies to more efficiently extract energy from a diet high in carbohydrates.