ORCID Profile
0000-0001-7096-3089
Current Organisation
INRA Centre de Montpellier
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Publisher: Cold Spring Harbor Laboratory
Date: 20-03-2018
DOI: 10.1101/282400
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 in idual sequencing data remains expensive for many non-model species, it has been shown that sequencing pools of in idual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of in idual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of F ST for 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 in idual DNAs to the pools. Last, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper , we show how the use of an unbiased F ST estimator may question the interpretation of population structure inferred from previous analyses.
Publisher: Wiley
Date: 03-2016
DOI: 10.1111/SYEN.12171
Publisher: Springer Science and Business Media LLC
Date: 29-07-2009
DOI: 10.1038/HDY.2009.102
Abstract: Recent advances in the statistical analysis of microsatellite data permit calculation of sex-specific dispersal rates through sex- and age-specific comparisons of genetic variation. This approach, developed for the analysis of data derived from co-dominant autosomal markers, should be applicable to a sex-specific marker such as mitochondrial DNA. To test this premise, we lified a 449 bp control region DNA sequence from the mitochondrial genome of the collared peccary (Pecari tajacu), and estimated intra-class correlations among herds s led from three Texas populations. Analyses on data partitioned by breeding group showed a clear signal of male-biased dispersal sex-specific fixation indices associated with genetic variation among social groups within populations yielded values for females (F(GP)=0.91), which were significantly larger than values for males (F(GP)=0.24 P=0.0015). The same general pattern emerged when the analyses were conducted on age classes (albeit nonsignificantly), as well as categories of in iduals that were predicted a posteriori to be dispersers (adult males) and philopatric (adult females and all immatures). By extending a previously published methodology based on biparentally inherited markers to matrilineally inherited haploid data, we calculated sex-specific rates of contemporary dispersal among social groups within populations (m(male symbol)=0.37). These results support the idea that mitochondrial DNA haplotype frequency data can be used to estimate sex-specific instantaneous dispersal rates in a social species.
Publisher: Springer Science and Business Media LLC
Date: 23-01-2013
Publisher: Wiley
Date: 02-2010
Publisher: Oxford University Press (OUP)
Date: 26-07-2018
DOI: 10.1534/GENETICS.118.300900
Abstract: The 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 in idual sequencing data remains expensive for many nonmodel species, it has been shown that sequencing pools of in idual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of in idual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of FST for 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 in idual DNAs to the pools. Finally, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased FST estimator may question the interpretation of population structure inferred from previous analyses.
No related grants have been discovered for Renaud Vitalis.