We estimated pairwise linkage disequilibrium (LD) as r2 in pure Populus trichocarpa and P. balsamifera, and a set of admixed individuals (see Appendix S1, Supporting Information), and detected haplotype blocks in the pure species using Haploview version 4.2 (Barrett et al. 2005) and the same phased genotypes used in RASPberry analysis. The decay of LD with physical distance was estimated following (Remington et al. 2001) and computing the expected values E(r2) with the formula from (Hill & Weir 1988) in an R script (http://www.r-project.org/).