Research ArticleGENETICS

Decline of genetic diversity in ancient domestic stallions in Europe

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Science Advances  18 Apr 2018:
Vol. 4, no. 4, eaap9691
DOI: 10.1126/sciadv.aap9691
  • Fig. 1 Stallion lineages through time.

    Temporal haplotype network of the four detected Y chromosome haplotypes. Age of the samples indicated by multiple layers separated by color; vertical lines connecting the haplotypes of consecutive layers/ages represent which haplotype was transferred into a later/younger period. Numbers constitute the respective number of individuals showing this particular haplotype for that period. Prz, Przewalski; Dom, domestic.

  • Fig. 2 Decline of paternal diversity began in Asia.

    Maps displaying age, locality, and haplotype (different colors) of each successfully genotyped sample.

  • Fig. 3 The frequencies of Y chromosome haplotypes started to change during the Late Bronze Age (1600–900 BCE).

    Inferred temporal trajectories of haplotype frequencies. Each haplotype is displayed by a different color. The shaded area represents the 95% highest-density region. The trajectories were constructed taking the median values across frequencies from the simulations of the Bayesian posterior sample. The small chart represents the stacked frequencies; the amplitude of each colored area is proportional to the median haplotype frequencies (normalized) at a given time. The x and y axes of the small chart match those in the large one. Ka, thousands of years.

  • Fig. 4 Positive selection for modern domestic haplotype leads to the decline of diversity.

    Violin plots of selection coefficients and initial haplotype frequencies, representing the posterior density functions of the selection coefficients of haplotypes Y-HT-1 and Y-HT-4, the age of Y-HT-1, and the initial haplotype frequencies of all haplotypes but Y-HT-1. The scale on the left is for the selection coefficients, whereas the scale on the right is for the age of Y-HT-1. The initial allele frequencies are on a scale from 0.0 (bottom) to 1.0 (top).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/4/eaap9691/DC1

    table S1. Additional information for all samples analyzed in this study.

    table S2. Genotyping results of Y chromosomal SNPs for successfully genotyped samples.

    table S3. Test of temporal changes in allele frequencies between the four time bins.

    table S4. Settings and operators of the MCMC procedure used for the final inference of selection coefficients and other parameters.

    fig. S1. Y-HT-1 showed very low allele frequency in early domestic horses.

    fig. S2. The three simulation approaches concur regarding a low initial Y-HT-1 frequency.

    fig. S3. All analyses yield strong support for positive selection of Y-HT-1.

    fig. S4. One selection coefficient for Y-HT-1 across all time periods was mostly supported.

    fig. S5. Several Y chromosome haplotypes were under selection.

  • Supplementary Materials

    This PDF file includes:

    • table S1. Additional information for all samples analyzed in this study.
    • table S2. Genotyping results of Y chromosomal SNPs for successfully genotyped samples.
    • table S3. Test of temporal changes in allele frequencies between the four time bins.
    • table S4. Settings and operators of the MCMC procedure used for the final inference of selection coefficients and other parameters.
    • fig. S1. Y-HT-1 showed very low allele frequency in early domestic horses.
    • fig. S2. The three simulation approaches concur regarding a low initial Y-HT-1 frequency.
    • fig. S3. All analyses yield strong support for positive selection of Y-HT-1.
    • fig. S4. One selection coefficient for Y-HT-1 across all time periods was mostly supported.
    • fig. S5. Several Y chromosome haplotypes were under selection.

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