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2017:courses:nourmohammad:start [2017/01/16 12:29] – created prado2017:courses:nourmohammad:start [2024/01/09 18:45] (current) – external edit 127.0.0.1
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 Molecular phenotypes, such as gene expression or protein binding affinities are important targets of natural selection, and are often subject to time-dependent pressure form the environment. However, the map between encoding DNA sequences and molecular phenotypes is often too difficult to quantify. In these lectures, I will show that universality is an emerging property of complex phenotypes, which are encoded by multiple genomic loci. I will introduce a non-equilibrium framework for adaptive dynamics of such phenotypes in time-dependent environments, and between co-evolving populations. In time-dependent environments, changes in the environment drive the evolution of the species, but not vice versa. As an example, I will present strong evidence that adaptation dominates the evolution of gene expression levels in Drosophila. Co-evolving populations reciprocally affect the fitness of each other, acting as time-dependent environments with feedback. As an example, I will show evidence of co-adaptation between interacting cellular populations of HIV viruses and the antibody repertoire of a patient over the course of an infection. In particular, I discuss the conditions for emergence of broadly neutralizing antibodies, which are recognized as critical for designing an effective vaccine against HIV. Molecular phenotypes, such as gene expression or protein binding affinities are important targets of natural selection, and are often subject to time-dependent pressure form the environment. However, the map between encoding DNA sequences and molecular phenotypes is often too difficult to quantify. In these lectures, I will show that universality is an emerging property of complex phenotypes, which are encoded by multiple genomic loci. I will introduce a non-equilibrium framework for adaptive dynamics of such phenotypes in time-dependent environments, and between co-evolving populations. In time-dependent environments, changes in the environment drive the evolution of the species, but not vice versa. As an example, I will present strong evidence that adaptation dominates the evolution of gene expression levels in Drosophila. Co-evolving populations reciprocally affect the fitness of each other, acting as time-dependent environments with feedback. As an example, I will show evidence of co-adaptation between interacting cellular populations of HIV viruses and the antibody repertoire of a patient over the course of an infection. In particular, I discuss the conditions for emergence of broadly neutralizing antibodies, which are recognized as critical for designing an effective vaccine against HIV.
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 +**References:**
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 +//i. Phenotype evolution under stabilizing selection//
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 +{{:2017:courses:nourmohammad:phenotype_stabilizingselection.pdf|}}
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 +//ii. Adaptive evolution of molecular phenotypes//
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 +{{:2017:courses:nourmohammad:phenotype_adaptation.pdf|}}
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 +//iii. Coevolution of phenotypes: antibody-viral interaction//
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 +main: {{:2017:courses:nourmohammad:coevolution.pdf|}}
 +SI: {{:2017:courses:nourmohammad:coevolution_si.pdf|}}
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2017/courses/nourmohammad/start.1484569769.txt.gz · Last modified: 2024/01/09 18:45 (external edit)