Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes. (11th November 2022)

• Record Type: Journal Article
• Authors: Linder, Robert A; Zabanavar, Behzad; Majumder, Arundhati; Hoang, Hannah Chiao-Shyan; Delgado, Vanessa Genesaret; Tran, Ryan; La, Vy Thoai; Leemans, Simon William; Long, Anthony D
• Editors: Zhang, Jianzhi
• Is Part Of: Molecular biology and evolution. Volume 39:Number 12(2022)
• Publication Date: 2022-11-11
• Subjects: yeast -- experimental evolution -- evolve and resequence -- complex traits; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msac248
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: We carried out a 200 generation Evolve and Resequence (E&R) experiment initiated from an outbred diploid recombined 18-way synthetic base population. Replicate populations were evolved at large effective population sizes (>10 5 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing resulted in an average between adjacent-gene per cell division recombination rate of ∼0.0008. Despite attempts to force weekly sex, roughly half of our populations evolved cheaters and appear to be evolving asexually. Focusing on seven chemical stressors and 55 total evolved populations that remained sexual we observed large fitness gains and highly repeatable patterns of genome-wide haplotype change within chemical challenges, with limited levels of repeatability across chemical treatments. Adaptation appears highly polygenic with almost the entire genome showing significant and consistent patterns of haplotype change with little evidence for long-range linkage disequilibrium in a subset of populations for which we sequenced haploid clones. That is, almost the entire genome is under selection or drafting with selected sites. At any given locus adaptation was almost always dominated by one of the 18 founder's alleles, with that allele varying spatially and between treatments, suggesting that selection acts primarily on rare variants private to a founder or haplotype blocks harboring multiple mutations.