Site frequency spectra observed in HIV populations
Zanini et al, eLife, 2015
Repeatability -- selecting 100 E. coli lines to live at 42C by Tenaillon et al
Extensive parallelism at the level of genes and pathways
Alternative adaptive path to heat adaptation
Drug resistance: repeated evolution of the same mutations is typical
Less well defined selection targets: repeatability is restricted to genes or pathways
Selection on quantitative traits: standing diversity determines response
Little success in a priori prediction of adaptive pathways
Predicting future populations
Future populations descend from present day high fitness individuals
Identify current high fitness individuals
Approach 1: leverage our understanding of trees of adapting populations (RN, Russell, Shraiman)
Approach 2: exploit historical patterns indicative of recent adaptation (Luksza and Lässig)
These methods now inform the WHO vaccine strain selection process.
Conclusions, limitations, questions
Good understanding of adapting populations under directional selection
Sequencing is easy, structure and function are hard
Limited ability to predict the nature of adaptations
Experimental evolution = artificial environments
→ atypical adaptation, dominated by loss of function mutations. Is this representative? Better/other systems?
Observable pathogen evolution → Coevolution.
Is this a more general setting (or limited RNA to viruses)?
Beyond one pathogen/one host?
Ecology gets in the way → coevolution, niche construction, variable environments
How does adaptation interact with ecology and intra-species partitioning?
Can we ever separate the environment from adaptation?
How does short term adaptation extrapolate to processes on longer time scales?