Multispecies pangenomes reveal a pervasive influence of population size on structural variation
Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs among three closely related species of North American jays (<i>Aphelocoma</i>, scrub-jays) displaying a 55-fold range in effective population size. We find rapid evolution of genome architecture, including ~100-megabase decreases in genome size driven by shifts in complex satellite landscapes. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with consistent evidence of adaptive fixation only in the largest population. Gene copy number variants exhibit an inverse relationship with population size, indicating strongly deleterious dynamics, with consequences for gene expression. Our long-read dataset and pangenome analysis demonstrate how population size shapes genome complexity.
Authors
- Nancy Chen (ORCID: https://orcid.org/0000-0001-8966-3449)
- Erik Garrison (ORCID: https://orcid.org/0000-0003-3821-631X)
- Danielle E. Khost (ORCID: https://orcid.org/0000-0001-6936-8864)
- Timothy B. Sackton (ORCID: https://orcid.org/0000-0003-1673-9216)
- George E. Kolyfetis (ORCID: https://orcid.org/0000-0002-9601-1526)
- Bohao Fang (ORCID: https://orcid.org/0000-0001-5283-067X)
- Devon A. DeRaad (ORCID: https://orcid.org/0000-0003-3105-985X)
- Andrea Guarracino (ORCID: https://orcid.org/0000-0001-9744-131X)
- Cameron K. Ghalambor (ORCID: https://orcid.org/0000-0003-2515-4981)
- Scott V. Edwards (ORCID: https://orcid.org/0000-0003-2535-6217)
- John E. McCormack (ORCID: https://orcid.org/0000-0002-0912-1461)
- Rebecca G. Cheek (ORCID: https://orcid.org/0000-0002-7935-3153)
- W. Chris Funk (ORCID: https://orcid.org/0000-0002-6466-3618)
- John W. Fitzpatrick (ORCID: https://orcid.org/0000-0002-6330-8403)
- Heng Li (ORCID: https://orcid.org/0000-0003-4874-2874)
Institutions
- Harvard University (US)
- University of Tennessee Health Science Center (US)
- University of California, Los Angeles (US)
- Norwegian University of Science and Technology (NO)
- Cornell University (US)
- Dana-Farber Cancer Institute (US)
- University of Rochester (US)
- Occidental College (US)
- Colorado State University (US)
Publication Details
- Journal
- Science
- Published
- 2025-12-11
- DOI
- https://doi.org/10.1126/science.adw1931
- Citations
- 2
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 1.61