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