Reconstruction of haplotype-blocks selected during experimental evolution.

Franssen, Susan U and Barton, Nicholas H and Schlötterer, Christian (2016) Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution, 34 (1). pp. 174-184. ISSN 0737-4038

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Official URL: http://dx.doi.org/10.1093/molbev/msw210

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.

Item Type: Article
DOI: 10.1093/molbev/msw210
Additional Information: This is a pre-copyedited, author-produced PDF of an article accepted for publication in Molecular Biology and Evolution following peer review. The version of record: Franssen S.U., Barton N.H., and Schlötterer C., "Reconstruction of haplotype-blocks selected during experimental evolution.", Molecular Biology and Evolution, vol. 34, Jan. 2016, 174-184. is available online at http://dx.doi.org/10.1093/molbev/msw210.
Uncontrolled Keywords: haplotype reconstruction, sequencing of pooled individuals (Pool-Seq), experimental evolution, replicated time series data, selection, evolve and resequence (E&R)
Subjects: 500 Science > 570 Life sciences; biology > 576 Genetics and evolution
Research Group: Barton Group
SWORD Depositor: Sword Import User
Depositing User: Sword Import User
Date Deposited: 23 Feb 2017 07:19
Last Modified: 30 Aug 2017 07:49
URI: https://repository.ist.ac.at/id/eprint/770

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