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  • ESEB2013 Poster Haplotype Methods Alexandra Vatsiou

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    Alexandra Vatsiou
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    This document compares five haplotype methods (iHS, EHHST, XP-EHH, XPCLR, XP-EHHST) to detect selection in populations under different scenarios. It tests the performance of each method with varying migration rates, recombination rates, and selection parameters. The results show that migration significantly impacts power, with iHS working best at high migration rates but false discovery rates still above 50%. XP-EHH and XPCLR worked as expected, while EHHST and XP-EHHST did not. XP-EHH was the only method to detect selection when the selected locus was not in the data, for a migration rate of 0.01. No method worked well for

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    This document compares five haplotype methods (iHS, EHHST, XP-EHH, XPCLR, XP-EHHST) to detect selection in populations under different scenarios. It tests the performance of each method with varying migration rates, recombination rates, and selection parameters. The results show that migration significantly impacts power, with iHS working best at high migration rates but false discovery rates still above 50%. XP-EHH and XPCLR worked as expected, while EHHST and XP-EHHST did not. XP-EHH was the only method to detect selection when the selected locus was not in the data, for a migration rate of 0.01. No method worked well for

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    57 vizualizări1 pagină

    ESEB2013 Poster Haplotype Methods Alexandra Vatsiou

    Încărcat de

    Alexandra Vatsiou
    This document compares five haplotype methods (iHS, EHHST, XP-EHH, XPCLR, XP-EHHST) to detect selection in populations under different scenarios. It tests the performance of each method with varying migration rates, recombination rates, and selection parameters. The results show that migration significantly impacts power, with iHS working best at high migration rates but false discovery rates still above 50%. XP-EHH and XPCLR worked as expected, while EHHST and XP-EHHST did not. XP-EHH was the only method to detect selection when the selected locus was not in the data, for a migration rate of 0.01. No method worked well for

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    din 1

    Comparison of Haplotype Methods to detect selection

    Alexandra I. Vatsiou, Christelle Melodelima, Eric Bazin, Oscar Gaggiotti Laboratoire d'Ecologie Alpine, University Joseph Fourier, Grenoble, France
    email: alex.vatsiou @ gmail.com

    Haplotype Methods that were compared


    Many methods take advantage of the increase of linkage disequilibrium and extent of haplotype homozygocity generated by selection. In this study we will compare five methods that have used this principle to detect selection. Our goal is to test the performance of each method under different scenarios of populations structure and different parameter values (migration, recombination and selection) iHS: Integrated Haplotype Score (1 population) (Voight et al.2007) EHHST: Extended haplotype-based homozygosity score test (1 population) (Zhong et al. 2010) XP-EHH: Cross Population Extended Haplotype Homozygosity (2 populations) (Sabeti et al. 2007) XPCLR: Cross population Composite Likelihood Ratio (2 populations) (Chen et al. 2010) XP-EHHST: Cross-population extended haplotype-based homozygosity score tests (2 populations) (Zhong et al. 2011)

    Test of robustness
    Population Structure
    Stepping Stone Model
    Y 2500 X 2500 W 2500

    Selection within population Y


    Initialize all the loci except locus 50 (monomorphic), sampling from the beta distribution

    Hard Sweep Burnin

    X 2500

    Insert a Mutated Allele at locus 50 within an individual.Set Positive Selection (s=0.1)

    Other Parameters Mutation rate: 10-7 Recombination Rate: 0.00375cM/kb No of loci: 101 Biallelic loci: 0 1 Selection model: 00 01 11 1+s 1+s/2 1

    Y 2500

    Z 2500

    OR
    W 2500

    tbegin
    Initialize all the loci, sampling from the beta distribution

    Generations

    tselection

    tend

    Island Model
    Z 2500

    Set Positive Selection (s=0.01)

    Soft Sweep

    Results (Hard Sweep & Island Model)


    Migration Rate 0.05 Migration Rate 0.01

    Discussion
    Migration affects the power significantly. iHS is the best test to use with high migration but still the FDR > 0.5. EHHST & XP-EHHST DO NOT work well. XP-EHH & XPCLR work as expected.

    Selected locus not in the data

    XP-EHH is the only test to detect the selected region if the selected locus is not in the data (migration=0.01). All the methods have the same pattern in a Stepping Stone as the Island Model No method worked well for a soft sweep. The analysis is a practical guideline to choose the most appropriate method.

    FUTURE:
    How the haplotype diversity & length evolves in a soft sweep?

    Selected locus not in the data

    REFS
    1. Chen, H., et al. (2010), ' Population differentiation as a test for selective sweeps.', Genome Research, 20 (3), 393-402. 2. Sabeti, P. C., et al. (2002), 'Detecting recent positive selection in the human genome from haplotype structure', Nature, 419 (6909), 832-7. 3. Sabeti, P. C., et al. (2007), 'Genome-wide detection and characterization of positive selection in human populations', Nature, 449 (7164), 913-8. 4. Voight, B. F., et al. (2006), 'A map of recent positive selection in the human genome', PLoS Biol, 4 (3), 72. 5. Zhong, M., et al. (2010), 'A powerful score test to detect positive selection in genome-wide scans', Eur J Hum Genet, 18 (10), 1148-59. 6. Zhong, M., et al. (2011), ' A cross-population extended haplotypebased homozygosity score test to detect positive selection in genomewide scans', Statistics and Its Interface, 4 (11), 5163.

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