Summary from the authors: Detecting selected haplotype blocks in evolve and resequence experiments

How organisms adapt to changes in the environment is not only a central question of evolutionary biology but also relevant to the threat of recent global warming. Evolution experiments in controlled laboratory settings (Experimental Evolution) are a great tool for evaluating evolutionary processes. When combined with genome sequencing (Evolve and Resequence), genomic changes related to adaptation can be identified. Although these genomic changes can occur in large parts of a chromosome (selected haplotype block), most approaches focus only on single genomic sites, and in consequence might overestimate the signal of evolution. Here, we present a novel method for detecting such selected haplotype blocks in evolve and resequence experiments. Our approach requires only few input parameters and is based on the grouping of neighboring genomic sites and on a comparison of different chromosomes. Analyzing computer simulations and experimental data, we describe distinct haplotype block patterns related to the number of genomic sites under selection and to the speed of adaptation. Our results indicate that the analysis of selected haplotype blocks has indeed the potential to deepen our understanding of adaptation.

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Figure 1: Left: Flies are a powerful model organism to study temperature adaptation from standing genetic variation in evolve and resequence experiments (modified from Mallard et al., 2018). Right: Selected haplotype blocks (blue) spanning large parts of a chromosome are present in the majority of individuals after 60 generations of experimental evolution.


Otte KA, Schlötterer C. Detecting selected haplotype blocks in evolve and resequence experiments. Mol Ecol Resour. 2021;21:93–109.

Mallard, François, et al. A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila. Genome biology 2018:19.1: 1-15.