Biology subjects

Andreas Wagner

Publications and source records attributed to Andreas Wagner.

3 recordsLinked to original sources

bioRxiv2016

Information theory and the phenotypic complexity of evolutionary adaptations and innovations

Two main lines of research link information theory to evolutionary biology. The first focuses on organismal phenotypes, and on the information that organisms acquire about their environment. The second connects information-theoretic concepts to genotypic change. The genotypic and phenotypic level can be linked by experimental high-throughput genotyping and computational models of genotype-phenotype relationships. I here use a simple information-theoretic framework to compute a phenotypes information content (its phenotypic complexity), and the information gain or change that comes with a new phenotype. I apply this framework to experimental data on DNA-binding phenotypes of multiple transcription factors. Low phenotypic complexity is associated with a biological systems ability to discover novel phenotypes in evolution. I show that DNA duplications lower phenotypic complexity, which illustrates how information theory can help explain why gene duplications accelerate evolutionary adaptation. I also demonstrate that with the right experimental design, sequencing data can be used to infer the information gain associated with novel evolutionary adaptations, for example in laboratory evolution experiments. Information theory can help quantify the evolutionary progress embodied in the discovery of novel adaptive phenotypes.

Evolutionary Biology↗

bioRxiv2016

The molecular chaperone DnaK accelerates protein evolution

Molecular chaperones, also known as heat-shock proteins, refold misfolded proteins and help other proteins reach their native conformation. Thanks to these abilities, some chaperones, such as the Hsp90 protein or the chaperonin GroEL, can buffer the deleterious phenotypic effects of mutations that alter protein structure and function. Hsp70 chaperones use a chaperoning mechanism different from Hsp90 and GroEL, and it is not known whether they can also buffer mutations. Here, we show that they can. To this end, we performed a mutation accumulation experiment in Escherichia coli, followed by whole-genome resequencing. Our sequence data shows that overexpression of the Hsp70 chaperone DnaK increases the tolerance of its clients for nonsynonymous nucleotide substitutions and nucleotide insertions and deletions. We also show that this elevated mutational buffering on short evolutionary time scales translates into differences in evolutionary rates on intermediate and long evolutionary time scales. To this end, we compared the evolutionary rates of DnaK clients and nonclients using the genomes of E. coli, Salmonella typhimurium, and 83 other gamma-proteobacterial species. We find that clients that interact strongly with DnaK evolve faster than weakly interacting clients. Our results imply that all three major chaperone classes can buffer mutations and affect protein evolution. They illustrate how an individual protein like a chaperone can have a disproportionate effect on proteome evolution.

Evolutionary Biology↗

bioRxiv2015

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

Tandem repeats (TR) are stretches of DNA that are highly variable in length and mutate rapidly, and thus an important source of genetic variation. This variation is highly informative for population and conservation genetics, and has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation have been scarce due to the technical difficulties derived from short-read technology.\n\nHere, we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, and their impact on gene expression evolution. We found that populations and species diversity patterns can be efficiently captured with short TRs (repeat unit length 1-5 base pairs) with potential applications in conservation genetics. We also examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length 2-50 base pairs). About one third of the 13,035 one-to-one orthologous genes contained TRs within 5 kilobase pairs of their transcription start site, and had higher expression divergence than genes without such TRs. The same observation held for genes with repeats in their 3 untranslated region, in introns, and in exons. Using our polymorphism data for the shortest TRs, we found that genes with polymorphic repeats in their promoters showed higher expression divergence in humans and chimpanzees compared to genes with fixed or no TRs in the promoters. Our findings highlight the potential contribution of TRs to recent human evolution through gene regulation.

Evolutionary Biology↗