Multispecies pangenomes reveal a pervasive influence of population size on structural variation

• 成果类型: Article
• 署名作者: Edwards, Scott V.; Fang, Bohao; Khost, Danielle; Kolyfetis, George E.; Cheek, Rebecca G.; Deraad, Devon A.; Chen, Nancy; Fitzpatrick, John W.; Mccormack, John E.; Funk, W. Chris; Ghalambor, Cameron K.; Garrison, Erik; Guarracino, Andrea; Li, Heng; Sackton, Timothy B.
• 署名单位: Harvard University; Harvard University; Harvard University; Colorado State University System; Colorado State University Fort Collins; University of California System; University of California Los Angeles; University of Rochester; Cornell University; Occidental College; Norwegian University of Science & Technology (NTNU); University of Tennessee System; University of Tennessee Health Science Center; Harvard University; Harvard University Medical Affiliates; Dana-Farber Cancer Institute
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-8075; 1095-9203
• DOI: 10.1126/science.adw1931
• 发表日期: 2025-12-11
• 页码: eadw1931
• 关键词: ADAPTIVE EVOLUTION; GENOMIC CONSEQUENCES; GENETIC MONOGAMY; APHELOCOMA JAYS; dna; mutations; rates; performance; inference; phylogeny

摘要

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 (Aphelocoma, scrub-jays) displaying a 55-fold range in effective population size. We find rapid evolution of genome architecture, including similar to 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.