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Fig. S1 Population structure in Populustrichocarpa based on 1000 randomly chosen Infinium SNP loci (one per candidate gene) and model-based clustering using v. 2.2 of the STRUCTURE program.

Fig. S2 Linear associations betweengenetic (FST, based on Infinium SNP data,22 280 loci) and geographic distances among subpopulations ofPopulus trichocarpa.

Fig. S3 Correspondence ofr2 values calculated based on estimated haplotype frequencies (i.e. using PHASE) to those based on genotypic correlations.

Fig. S4 Effect of population structure onestimates of linkage disequilibrium (LD r2) basedon genome resequencing and Infinium SNP data (a) and LD-basedestimates of effective population size (Ne) fromgenome resequencing data (b).

Fig. S5 Linkage disequilibrium for physically unlinked loci.

Fig. S6 Correlates of recombination inP.  trichocarpa.

Fig. S7 Recombination rates in 1-Mb windows estimated from a dense SNP linkage map and from genome resequencing data.

Table S1 Summary of genome resequencingdata for 16 Populus trichocarpa trees

Table S2 Summary statistics for Sangerresequencing data for 10 candidate genes in 47P.  trichocarpa trees

Table S3 Genetic (below diagonal,FST, based on Infinium SNP data, 22 280loci) and geographic (above diagonal, km) distances among 10subpopulations of Populus trichocarpa

Table S4 100-kb window correlation matrixof recombination correlates in Populus trichocarpa

Table S5 1-Mb window correlation matrix ofrecombination correlates in Populus trichocarpa

Table S6 Multiple linear regression modelfor log10 (4Nec) analyzed in 100-kbwindows

Table S7 Multiple linear regression modelfor log10(4Nec) analyzed in 1-Mbwindows

Methods S1 Infinium SNP data.

Methods S2 Correlates of recombination.

Methods S3 Estimates of effective population size from linkage disequilibrium.

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