ArticleProceedings of the National Academy of Sciences of the United States of America2010
Polygenic and directional regulatory evolution across pathways in Saccharomyces.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed.
- Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses.Nature communications · 2026Article
- Gene-by-environment Interactions and Adaptive Body Size Variation in Mice From the Americas.Molecular biology and evolution · 2025Article
- Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes.Heredity · 2024Article
- Extensive transcriptome data providing great efficacy in genetic research and adaptive gene discovery: a case study ofFrontiers in plant science · 2024Article
- Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks.Molecular biology and evolution · 2023Article
- Mechanisms of regulatory evolution in yeast.Current opinion in genetics & development · 2022Review
- Article
- Population and comparative genetics of thermotolerance divergence between yeast species.G3 (Bethesda, Md.) · 2021Article
- Lineage-specific selection and the evolution of virulence in theProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Divergence of Peroxisome Membrane Gene Sequence and Expression Between Yeast Species.G3 (Bethesda, Md.) · 2020Article
- Regulation and metabolic engineering strategies for permeases of Saccharomyces cerevisiae.World journal of microbiology & biotechnology · 2019Review
- Intrinsic cooperativity potentiates paralleleLife · 2018Article
- Neutral Theory and Phenotypic Evolution.Molecular biology and evolution · 2018Article
- Testing the neutral hypothesis of phenotypic evolution.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Coordinated Functional Divergence of Genes after Genome Duplication inThe Plant cell · 2017Article
- Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast).Molecular biology and evolution · 2017Article
- High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites.PLoS genetics · 2017Article
- Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids.Scientific reports · 2017Article
- Gene expression and adaptive noncoding changes during human evolution.BMC genomics · 2017Article
- Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species.Genome biology and evolution · 2017Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The search to understand how genomes innovate in response to selection dominates the field of evolutionary biology. Powerful molecular evolution approaches have been developed to test individual loci for signatures of selection. In many cases, however, an organism's response to changes in selective pressure may be mediated by multiple genes, whose products function together in a cellular process or pathway. Here we assess the prevalence of polygenic evolution in pathways in the yeasts Saccharomyces cerevisiae and S. bayanus. We first established short-read sequencing methods to detect cis-regulatory variation in a diploid hybrid between the species. We then tested for the scenario in which selective pressure in one species to increase or decrease the activity of a pathway has driven the accumulation of cis-regulatory variants that act in the same direction on gene expression. Application of this test revealed a variety of yeast pathways with evidence for directional regulatory evolution. In parallel, we also used population genomic sequencing data to compare protein and cis-regulatory variation within and between species. We identified pathways with evidence for divergence within S. cerevisiae, and we detected signatures of positive selection between S. cerevisiae and S. bayanus. Our results point to polygenic, pathway-level change as a common evolutionary mechanism among yeasts. We suggest that pathway analyses, including our test for directional regulatory evolution, will prove to be a relevant and powerful strategy in many evolutionary genomic applications.
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