Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow
The study of local adaptation is a main focus of evolutionary biology since it may contribute to explain the current species diversity. The genomic scan procedures permit for the first time to study the connection between specific DNA patterns and processes as natural selection, genetic drift, recom...
| Main Authors: | , , |
|---|---|
| Format: | Online |
| Language: | English |
| Published: |
Bentham Science Publishers
2015
|
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460224/ |
| id |
pubmed-4460224 |
|---|---|
| recordtype |
oai_dc |
| spelling |
pubmed-44602242015-12-01 Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow Rivas, M. J. Domínguez-García, S. Carvajal-Rodríguez, A. Article The study of local adaptation is a main focus of evolutionary biology since it may contribute to explain the current species diversity. The genomic scan procedures permit for the first time to study the connection between specific DNA patterns and processes as natural selection, genetic drift, recombination, mutation and gene flow. Accordingly, the information on genomes from non-model organisms increases and the interest on detecting the signal of natural selection in the DNA sequences of different populations also raises. The main goal of the present work is to explore a sequence-based method for detecting natural selection in divergent populations connected by migration. In doing so, we rely on a recently published statistic based upon th e definition of haplotype allelic classes (HAC). The original measure was modified to be more sensitive to intermediate frequencies in non-model species. A linkage-disequilibrium-based method was also assayed and individual-based simulations were performed to test the methods. The results suggest that the HAC-based methods and, specifically, the new proposed method are quite powerful for detecting the footprint of moderate divergent selection. They are also robust to reasonable model misspecification. One obvious advantage of the new algorithm is that it does not require knowledge of the allelic state. Bentham Science Publishers 2015-06 2015-06 /pmc/articles/PMC4460224/ /pubmed/26069460 http://dx.doi.org/10.2174/1389202916666150313230943 Text en © 2015 Bentham Science Publishers http://creativecommons.org/licenses/by-nc/3.0/ This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Rivas, M. J. Domínguez-García, S. Carvajal-Rodríguez, A. |
| spellingShingle |
Rivas, M. J. Domínguez-García, S. Carvajal-Rodríguez, A. Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow |
| author_facet |
Rivas, M. J. Domínguez-García, S. Carvajal-Rodríguez, A. |
| author_sort |
Rivas, M. J. |
| title |
Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow |
| title_short |
Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow |
| title_full |
Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow |
| title_fullStr |
Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow |
| title_full_unstemmed |
Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow |
| title_sort |
detecting the genomic signature of divergent selection in presence of gene flow |
| description |
The study of local adaptation is a main focus of evolutionary biology since it may contribute
to explain the current species diversity. The genomic scan procedures permit for the first time to study
the connection between specific DNA patterns and processes as natural selection, genetic drift, recombination,
mutation and gene flow. Accordingly, the information on genomes from non-model organisms
increases and the interest on detecting the signal of natural selection in the DNA sequences of different
populations also raises. The main goal of the present work is to explore a sequence-based method
for detecting natural selection in divergent populations connected by migration. In doing so, we rely
on a recently published statistic based upon th e definition of haplotype allelic classes (HAC). The original
measure was modified to be more sensitive to intermediate frequencies in non-model species. A linkage-disequilibrium-based method was also assayed and individual-based simulations were performed to test the methods. The
results suggest that the HAC-based methods and, specifically, the new proposed method are quite powerful for detecting
the footprint of moderate divergent selection. They are also robust to reasonable model misspecification. One obvious advantage
of the new algorithm is that it does not require knowledge of the allelic state. |
| publisher |
Bentham Science Publishers |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460224/ |
| _version_ |
1613233256026603520 |