Table of Contents for analyses in "Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples"¶

by Biddanda, Steinrücken, and Novembre¶

  1. Main Analyses

    • Probability of uncoupling & correlation of pairwise differences
    • Correlation in pairwise differences with time-stratified sampling
    • Correlation in pairwise differences in ancient WGS data
    • Calculation of joint-LD with time-stratified sampling
    • Haplotype copying jump-rates under varying demographies
    • Haplotype copying jump-rates estimated in 1240K ancient DNA data
  2. Supplementary Analyses

    • The impact of population divergence on two-locus variation patterns
    • Time to first coalescence for an ancient sample with a member of the modern panel
    • Verifying Li-Stephens Jump Rate MLE inference
    • Estimating $t_a$ and $N_e$ from $Corr(\pi_A,\pi_B)$
    • Time to first coalescent for ancient sample with instant growth
    • The impact of growth and bottleneck strength on the correlation in branch length
    • Schematic plots
    • Validating Two-Locus Equations via Two-Locus Simulations