The dynamics of adaptation to stress from standing genetic variation andde novomutations

Abstract

Adaptation from standing genetic variation is an important process underlying evolution in natural populations but we rarely get the opportunity to observe the dynamics of fitness changes in real time. Here, we used the power of microbial experimental evolution and whole population sequencing to track the phenotypic and genomic changes of genetically diverse yeast populations in environments with different stress levels. We found that populations rapidly and in parallel increased in fitness in stressful environments. The founder's genetic diversity was quickly depleted, however, not to the same degree in all populations and environments. Some populations fixed all ancestral variation in < 30 generations while others maintained diversity across hundreds of generations. We also observed parallelism at the gene and pathway level. Specifically, we detected up to seven genes harbouring multiple independent mutations in different populations, and a general enrichment for mutations affecting downstream effectors of the high-osmolarity-glycerol pathway in three out of four environments. Adaptation to the most stressful environment was characterised by the fast evolution of functional haploidy, likely driven by standing genetic variation. Almost 40% of all populations contained aneuploidies (losses or gains of chromosomes) at least once during experimental evolution. Some aneuploidies were maintained for hundreds of generations in parallel in different replicates, suggesting they were adaptive. This work shows that experimental evolution is a great tool to address the interplay between standing variation and the influx of de novo mutations, leading to a better understanding of the demographic and environmental drivers and constraints of a population's capacity to adapt to environmental change.

Network architecture of transcriptomic stress responses in zebrafish embryos

“…Genetic networks are often used in human research (Rual et al 2005; Luck et al 2020). Additional studies have focused on network evolution in fungi (Joy et al 2005; Usaj et al 2017; Lorena Ament-Velásquez et al 2022; Wollenberg Valero 2020) and bacteria (Philippe et al 2007; Crombach and Hogeweg 2008), with very few studies pertaining to vertebrate animals (but see (Wollenberg Valero et al 2014, 2022) for examples of climate adaptation-related networks). However, a few general patterns are emerging; such as that of genes towards the center of the network being most highly conserved, and those positioned intermediately having the highest number of connections with other nodes, whereas both constraint and pleiotropy are lowest at the network periphery (also see (Wollenberg Valero 2024).…”

Loss of Heterozygosity and Its Importance in Evolution

“…Towards this goal, the community has identified and linked changes in ploidy, copy number variants, aneuploidy, and single nucleotide variants to fitness in a number of different organisms, but particularly in microbial systems like E. coli and S. cerevisiae (Lenski 2017 ; McDonald 2019 ). While many experimental design setups of microbial systems are done in homozygous haploids or diploids, an increasing number of experiments have utilized heterozygous intraspecific (Ament-Velásquez et al 2022 ; Burke et al 2014 ; Phillips et al 2020 , 2022 ; Smukowski Heil et al 2017 , 2019 ; Wing et al 2020 ) and/or interspecific hybrids (Bautista et al 2021 ; Charron et al 2019 ; Dunn et al 2013 ; Peris et al 2020 ; Piotrowski et al 2012 ; Smukowski Heil et al 2017 , 2019 ; Vázquez-García et al 2017 ). Heterozygous strain backgrounds introduce more complex genetic variation and interactions, and can better represent dynamics relevant in a number of natural and anthropogenic environments.…”