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Figure S1. Schematic demonstration of the thresholds used to assign the four genotype classes: pure P. balsamifera (B), pure P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). Reference populations were used as an a priori learning population to develop threshold levels to assign individuals from BPSF. Individuals above the upper threshold were considered pure. If Q-values fell below the lower threshold, then alleles for that species were absent within an individual. Genotype classes were based on Q-values and CI intervals relative to the 0.5 threshold (i.e., F1) and the lower threshold (backcrosses or trihybrids).

Figure S2. Box plot of adult tree diameter at breast height (DBH) and height for four genotype classes: pure P. balsamifera (B), pure P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). Post-hoc tests (Tukey contrasts) were used to identify differences among genotype class means.

Figure S3. Box plot of adult tree reproductive biomass and yield for four genotype classes: pure P. balsamifera (B), pure P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). Reproductive biomass measures include: total biomass, seed biomass, 100-seed biomass, capsule biomass, stem biomass, cotton biomass. Reproductive yield measures: number of capsules per catkin, seeds per capsule, and seeds per catkin. Post-hoc tests (Tukey contrasts) were used to identify differences among genotype class means.

Figure S4. Box plot of adult tree seed viability for four genotype classes: pure P. balsamifera (B), pure P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). Seed viability was assessed based on percent germination and percent abnormal germinants. Post-hoc tests (Tukey contrasts) were used to identify differences among genotype class means.

Figure S5. Box plot of adult tree disease susceptibility for four genotype classes: pure P. balsamifera (B), pure P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). Disease susceptibility was assessed based on the number of uredia per cm2 for using controlled inoculations of three Melampsora species. Post-hoc tests (Tukey contrasts) were used to identify differences among genotype class means.

ece31028-sup-0002-File1-10.docWord document303K

Data S1. R code for statistical analyses.

Table S1. Diagnostic SNP markers for native and exotic poplar species at Base de plein-air de Sainte-Foy (Table adapted from Isabel et al. 2013). Major allele frequency is 1.0 unless indicated otherwise. Gray cells indicate the potential presence of a partial null allele. Populus trichocarpa Nisqually-1 was used as a reference sequence.

Table S2. Summary of half-sibling progeny from pure, hybrid, and exotic hybrid mothers. Putative fathers are inferred by haplotype substraction from maternal and seed genotypes (P. balsamifera = B, P. deltoides = D, P. nigra = N, P. maximowiczii = M; ? indicates that the father genotype could not be completely reconstructed with confidence).

Table S3. Distribution of age classes estimated for reproductively mature P. balsamifera, P. deltoides, and native hybrids at Base de plein-air de Sainte-Foy.

Table S4. Number of poplar trees measured for reproductive fitness and disease resistance traits: reproductive biomass, reproductive yield, seed viability, fungal disease susceptibility. Fungal disease was measure for three Melampsora species: M. larici-populina (Mlp), M. medusae f.sp. deltoidea (Mmd), and M. occidentalis (Mo).Trees were grouped into four genotypic classes: pure P. balsamifera (B), pure P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). Numbers in brackets indicate the number of trees sampled more than once.

Table S5. Linear mixed-effects model analysis summary for six biomass measurments taken on catkins from trees in P. balsamifera (B), P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). A: Full data set; B: Partial data set of once sampled trees. Post-hoc tests (Tukey contrasts) were used to identify differences among genotype class means.

Table S6. Linear mixed-effects model analysis summary for the reproductive yield of catkins sampled in P. balsamifera (B), P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). 7A: Full data set; 7B: Partial data set. Post-hoc tests (Tukey contrasts) were used to identify differences among tree class means when a significant fixed effect was detected.

Table S7. General linear model analysis summary for germination of seed from trees in four genotype classes: pure P. balsamifera (B), P. deltoides (D), native hybrids (D × B), and exotic hybrids (X). Tukey's Honestly Significant Difference test was used to identify differences among genotype class means when a significant effect was detected (Table 2).

Table S8. Linear mixed-effects model analysis summary for infection severity (number of uredia) of poplar rust on trees in four genotypic classes: pure P. balsamifera, pure P. deltoides, native hybrids, and exotic hybrids. Results are based on controlled inoculations of Melampsora larici-populina (Mlp), M. medusae f.sp. deltoidae (Mmd), and M. occidentalis (Mo). Tukey's Honestly Significant Difference test was used to identify differences among genotype class means when a significant fixed effect was detected (shown in Table 2).

Table S9. Field surveys of fungal disease at Base de plein-air de Sainte-Foy. Melampsora spp. incidence was recorded as one of three damage classes: absent, <50% leaf area, and >50% leaf area. Septoria spp. leaf spot was recorded as presence or absence. Proportion of observed trees in each class is shown in brackets.

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