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Genomics and the origin of species
Emergent trends and gaps in understanding are identified, new approaches to more fully integrate genomics into speciation research are proposed, and an integrative definition of the field of speciation genomics is provided.
The Limits to Parapatric Speciation: Dobzhansky–Muller Incompatibilities in a Continent–Island Model
The maximum rate of gene flow is limited by exogeneous selection, and there are two distinct mechanisms that drive DMI evolution in parapatry, selection against immigrants in a heterogeneous environment and selection against hybrids due to the incompatibility.
SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS
- Ryan T. Hietpas, C. Bank, J. Jensen, D. Bolon
- BiologyEvolution; international journal of organic…
- 1 December 2013
It is demonstrated that an essential protein can harbor adaptive potential upon an environmental challenge, and a remarkable fit of the data is reported to a version of Fisher's geometric model that focuses on the fitness trade‐offs between mutations in different environments.
Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective
Evaluating whole-genome datasets of an influenza A H1N1 strain in the presence and absence of oseltamivir collected at thirteen time points reveals a striking consistency, and results suggest the ability to predict certain aspects of viral evolution in response to changing host environments and novel selective pressures.
A systematic survey of an intragenic epistatic landscape
The distribution of intragenic epistatic effects within this region in seven Hsp90 point mutant backgrounds of neutral to slightly deleterious effect is reported and discussed, resulting in an analysis of more than 1000 double-mutants.
Thinking too positive? Revisiting current methods of population genetic selection inference.
A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments
A Bayesian MCMC approach to estimate fitness from deep sequencing data and using it to assess the DFE for the same 560 point mutations in a coding region of Hsp90 in Saccharomyces cerevisiae across six different environmental conditions shows that multiple-step mutations harbor more potential for adaptation in challenging environments, but also tend to be more deleterious in the standard environment.
On the (un)predictability of a large intragenic fitness landscape
- C. Bank, S. Matuszewski, Ryan T. Hietpas, J. Jensen
- BiologyProceedings of the National Academy of Sciences
- 18 November 2016
A uniquely large multiallelic fitness landscape comprising 640 engineered mutants that represent all possible combinations of 13 amino acid-changing mutations at 6 sites in the heat-shock protein Hsp90 in Saccharomyces cerevisiae under elevated salinity is presented.
A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance.
The fitness landscape of the codon space across environments
- I. Fragata, S. Matuszewski, Mark A. Schmitz, T. Bataillon, J. Jensen, C. Bank
- 23 January 2018
A new software based on Bayesian Monte Carlo Markov Chain methods is used and re-estimate selection coefficients of all possible codon mutations across 9 amino acid positions in Saccharomyces cerevisiae Hsp90 across 6 environments to highlight a possible role of synonymous mutations in adaptation and indicate the potential mis-inference when they are neglected in fitness landscape studies.