Reconstruction of haplotype-blocks selected during experimental evolution.

S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.

Download
OA IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf 295.27 KB
OA IST-2017-770-v1+2_Fig1.pdf 10.90 MB
OA IST-2017-770-v1+3_Fig2.pdf 21.44 KB
All

Journal Article | Published | English

Scopus indexed
Author
Franssen, Susan; Barton, Nick HIST Austria ; Schlötterer, Christian
Department
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.
Publishing Year
Date Published
2016-10-03
Journal Title
Molecular Biology and Evolution
Acknowledgement
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”.
Volume
34
Issue
1
Page
174 - 184
IST-REx-ID

Cite this

Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210
Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution, 34(1), 174–184. https://doi.org/10.1093/molbev/msw210
Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution 34, no. 1 (2016): 174–84. https://doi.org/10.1093/molbev/msw210.
S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1, pp. 174–184, 2016.
Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.
Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.
All files available under the following license(s):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Main File(s)
Access Level
OA Open Access
Date Uploaded
2018-12-12
MD5 Checksum
1e78d3aaffcb40dc8b02b7b4666019e0
File Name
Access Level
OA Open Access
Date Uploaded
2018-12-12
MD5 Checksum
e13171843283774404c936c581b4543e
File Name
Access Level
OA Open Access
Date Uploaded
2018-12-12
MD5 Checksum
63bc6e6e61f347594d8c00c37f874a0b
Access Level
OA Open Access
Date Uploaded
2018-12-12
MD5 Checksum
da87cc7c78808837f22a3dae1c8397f9
File Name
Access Level
OA Open Access
Date Uploaded
2018-12-12
MD5 Checksum
e47b2a0c32142f423b3100150c0294f8
File Name
Access Level
OA Open Access
Date Uploaded
2018-12-12
MD5 Checksum
a5a7d6b32e7e17d35d337d7ec2a9f6c9


Export

Marked Publications

Open Data IST Research Explorer

Search this title in

Google Scholar