Reconstruction of haplotype-blocks selected during experimental evolution. Journal Article

Author(s): Franssen, Susan U; Barton, Nicholas H; Schlötterer, Christian
Article Title: Reconstruction of haplotype-blocks selected during experimental evolution.
Affiliation IST Austria
Abstract: The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles.
Keywords: haplotype reconstruction, sequencing of pooled individuals (Pool-Seq), experimental evolution, replicated time series data, selection, evolve and resequence (E&R)
Journal Title: Molecular Biology and Evolution
Volume: 34
Issue 1
ISSN: 0737-4038
Publisher: OUP  
Date Published: 2016-01-01
Start Page: 174
End Page: 184
DOI: 10.1093/molbev/msw210
Notes: The authors thank all members of the Institute of Population Genetics for discussion and support on the project and par- ticularly N. Barghi for helpful comments on earlier versions of the manuscript. This work was supported by the European Research Council (ERC) grants “ArchAdapt” and “250152”.
Open access: yes (repository)