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A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
Open accessAbstract
Identifying loci under natural selection from genomic surveys is of great interest in different research areas. Commonly used methods to separate neutral effects from adaptive effects are based on locus-specific population differentiation coefficients to identify outliers. Here we extend such an approach to estimate directly the probability that each locus is subject to selection using a Bayesian method. We also extend it to allow the use of dominant markers like AFLPs. It has been shown that this model is robust to complex demographic scenarios for neutral genetic differentiation. Here we show that the inclusion of isolated populations that underwent a strong bottleneck can lead to a high rate of false positives. Nevertheless, we demonstrate that it is possible to avoid them by carefully choosing the populations that should be included in the analysis. We analyze two previously published data sets: a human data set of codominant markers and a Littorina saxatilis data set of dominant markers. We also perform a detailed sensitivity study to compare the power of the method using amplified fragment length polymorphism (AFLP), SNP, and microsatellite markers. The method has been implemented in a new software available at our website (http://www-leca.ujf-grenoble.fr/logiciels.htm).
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Citations
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“Early methods for differentiation outlier detection assumed that the study system followed the island model (assumed by fdist2 [Beau-mont and Nichols 1996]; table A1) or a multinomial Dirichlet distribution (e.g., BayeScan [Foll and Gaggiotti 2008]; table A1).”
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“%) were scored as outliers across the three methods performed by BAYESCAN 2.1 [25, 26] and MCHEZA [27].”
BackgroundMethodInfluentialGenetic and Epigenetic Differentiation in Response to Genomic Selection for Avian Lay Date
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Metadata
- Authors
- Foll, M., & Gaggiotti, O.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-10-01
- Volume
- 180
- Issue
- 2
- Pages
- 977-993
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2162157671
- Cited by
- 2,736
- References
- 0
- FWCI
- 27.25
- Type
- journal article
- Language
- en
- Open access
- bronze
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