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Measuring Genetic Differentiation from Pool-seq Data
- Source :
- Genetics, Genetics, Genetics Society of America, 2018, 210 (1), pp.315-330. ⟨10.1534/genetics.118.300900⟩, Genetics, 2018, 210 (1), pp.315-330. ⟨10.1534/genetics.118.300900⟩, Genetics 1 (210), 315-330. (2018)
- Publication Year :
- 2018
-
Abstract
- The recent advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many non-model species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator ofFSTfor Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased, and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Last, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpinCottus asper, we show how the use of an unbiasedFSTestimator may question the interpretation of population structure inferred from previous analyses.
- Subjects :
- 0106 biological sciences
0301 basic medicine
population genomics
Genotype
F-ST
genetic differentiation
pool sequencing
Computational biology
Biology
Investigations
010603 evolutionary biology
01 natural sciences
Polymorphism, Single Nucleotide
DNA sequencing
Population genomics
03 medical and health sciences
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems
Gene Frequency
[SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology
Databases, Genetic
Genetics
Computer Simulation
Genotyping
ComputingMilieux_MISCELLANEOUS
Alleles
030304 developmental biology
0303 health sciences
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
Estimator
Robustness (evolution)
Genetic Variation
High-Throughput Nucleotide Sequencing
DNA
Genomics
Sequence Analysis, DNA
biology.organism_classification
Genetic differentiation
[SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology
030104 developmental biology
Genetic structure
Cottus asper
[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Subjects
Details
- ISSN :
- 19432631 and 00166731
- Volume :
- 210
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Genetics
- Accession number :
- edsair.doi.dedup.....db306bfd1891445b1fd61824b710a4ed