---
_id: '1195'
abstract:
- lang: eng
text: '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. '
acknowledgement: "The authors thank all members of the Institute of Population\r\nGenetics
for discussion and support on the project and par-\r\nticularly N. Barghi for helpful
comments on earlier versions of\r\nthe manuscript. This work was supported
\ by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”."
article_processing_charge: No
author:
- first_name: Susan
full_name: Franssen, Susan
last_name: Franssen
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Christian
full_name: Schlötterer, Christian
last_name: Schlötterer
citation:
ama: 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
apa: Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of
haplotype-blocks selected during experimental evolution. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210
chicago: Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction
of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology
and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.
ieee: S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks
selected during experimental evolution.,” Molecular Biology and Evolution,
vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.
ista: Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks
selected during experimental evolution. Molecular Biology and Evolution. 34(1),
174–184.
mla: 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.
short: S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution
34 (2016) 174–184.
date_created: 2018-12-11T11:50:39Z
date_published: 2016-10-03T00:00:00Z
date_updated: 2025-09-22T09:43:41Z
day: '03'
ddc:
- '576'
department:
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doi: 10.1093/molbev/msw210
ec_funded: 1
external_id:
isi:
- '000396772000009'
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call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Biology and Evolution
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publisher: Oxford University Press
publist_id: '6155'
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title: Reconstruction of haplotype-blocks selected during experimental evolution.
type: journal_article
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volume: 34
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...