DNA replication errors are a major source of adaptive gene amplification

Abstract

Detecting and understanding heritable changes in DNA that contribute to adaptive evolution is a primary goal of evolutionary biology. Copy number variants (CNVs)—gains and losses of genomic sequences—are an important source of genetic variation underlying rapid adaptation and genome evolution. However, despite their central role in evolution little is known about the factors that contribute to the structure, size, formation rate, and fitness effects of adaptive CNVs. Local genome elements are likely to be an important determinant of these properties. Whereas it is known that point mutation rates vary with genomic location and local sequence features, the role of genome architecture in the formation, selection, and the resulting evolutionary dynamics of CNVs is poorly understood. Previously, we have found that the GAP1 gene in Saccharomyces cerevisiae undergoes frequent and repeated amplification and selection under long-term experimental evolution in glutamine-limiting conditions. The GAP1 gene has a unique genomic architecture consisting of two flanking long terminal repeats (LTRs) and a proximate origin of DNA replication (autonomously replicating sequence, ARS), which are likely to promote rapid GAP1 CNV formation. To test the role of these genomic elements on CNV-mediated adaptive evolution we performed experimental evolution in glutamine-limited chemostats using engineered strains lacking either the adjacent LTRs, ARS, or all elements. Using a CNV reporter system and neural network simulation-based inference (nnSBI) we quantified the formation rate and fitness effect of CNVs for each strain. We find that although GAP1 CNVs repeatedly form and sweep to high frequency in all strains, removal of local DNA elements significantly impacts the rate and fitness effect of CNVs and the rate of adaptation. We performed genome sequence analysis to define the molecular mechanisms of CNV formation for 177 CNV lineages. We find that 49% of all GAP1 CNVs are mediated by the DNA replication-based mechanism Origin Dependent Inverted Repeat Amplification (ODIRA) regardless of background strain. In the absence of the local ARS, a distal ARS can mediate ODIRA CNV formation. In the absence of local LTRs homologous recombination mechanisms still mediate gene amplification following de novo insertion of retrotransposon elements at the locus. Our study demonstrates the remarkable plasticity of the genome and reveals that DNA replication errors are a predominant source of adaptive CNVs.