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Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam… Suarez-Gonzalez, Adriana; Hefer, Charles A.; Christe, Camille; Corea, Oliver; Lexer, Christian; Cronk, Quentin C. B.; Douglas, Carl J. 2016-04

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  Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood).  Adriana Suarez-Gonzalez1, Charles A. Hefer1,4, Camille Christe2, Oliver Corea3, Christian Lexer2,5, Quentin C. B. Cronk1 and Carl J. Douglas1*   1Department of Botany, University of British Columbia, Vancouver, Canada 2 Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland 3 Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada; 4 Current address: Biotechnology Platform, Agricultural Research Council, Private Bag X05, Onderstepoort, 0110, South Africa  5 Department of Botany and Biodiversity Research, University of Vienna, Austria  Keywords: Adaptive introgression, Populus, local adaptation, admixture   *Corresponding author: Carl J. Douglas Email: carl.douglas@ubc.ca Phone: +1 604-822-2618 Running head: Adaptive introgression in Populus   ABSTRACT Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species P. balsamifera and identified candidate genes for local adaptation. Here, we explored patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular, or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or sub-functionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.    INTRODUCTION Introgression between recently diverged species with incomplete reproductive barriers is a widespread process that can provide novel genetic recombinants and promote adaptation to new environments (Arnold 2006). Although stochastic processes such as genetic drift are main drivers underlying the geographic distribution of genetic regions introduced by introgressive hybridization, natural selection also plays an important role when adaptive genes are exchanged across species boundaries (Barton & Gale 1993; The Heliconius Genome Consortium 2012; Hamilton et al. 2013; Abbott et al. 2013). For instance, hybridization can contribute to adaptive genetic variation if recombination leads to the introgression of genomic regions with modular, or cassette-like variation, i.e. multiple linked mutations across blocks of genes, associated with adaptive traits (Abbott et al. 2013).   Forest tree species are attractive targets to study adaptive introgression largely because they exhibit extensive natural hybrid zones (Lexer et al. 2004), but also because of their large ranges across geographical and climatic clines, as well as substantial trait variation (Savolainen et al. 2007; Soolanayakanahally et al. 2009; Keller et al. 2011; McKown et al. 2013). Research on the contribution of interspecific hybridization and introgression to local adaptation is rapidly expanding in long-lived tree species [e.g spruce (de Lafontaine et al. 2015; Hamilton et al. 2014), Eucalyptus (Larcombe et al. 2015), and oak (Abadie et al. 2012)]. However, studies documenting fine-scale introgression patterns within and around target genes, and identifying adaptive introgression at the gene level have mainly focused on taxa with short generation spans in both plants and animals [(Whitney et al. 2015; Martin et al. 2006; Wang et al. 2014; The Heliconius Genome Consortium 2012; Norris et al. 2015) but see (Martinsen et al. 2001; Lind-  Riehl et al. 2014; Racimo et al. 2015)], and have not been carried out in tree species. The characterization of population-wide genomic diversity in keystone or foundation forest tree species will enable the study of species complexes involving ecologically divergent yet hybridizing taxa (Lexer et al. 2004; Buerkle & Lexer 2008), to explicitly test for adaptive introgression at a fine genomic scale. Such genomic scans could be used to identify genomic regions that are more prone to introgression than others, potentially underlying adaptive processes. Clarifying the magnitude and impact of introgressed genes contributing to functionally relevant variation in trees has great potential for forest ecology, management, and restoration efforts in the face of climate change (Lexer et al. 2004; Whitham et al. 2006; Hamilton & Miller, 2015).  Buerkle and Lexer (2008) proposed using admixture mapping, a gene mapping method for traits that differ in frequency across populations, to reveal genomic regions associated with adaptation. Recent applications of this approach to trees has provided a first glimpse of the genetic architecture of ecologically important traits (Caseys et al. 2015; Lindtke et al. 2013), but much higher marker densities and more highly recombinant mapping populations are required to obtain precise map locations of candidate genes.  Based on the large-scale characterization of genomic diversity in wild populations of Populus, trees of this genus have emerged as an important model for population genomic studies of adaptation (Weigel & Nordborg 2015). Here, we used such data from P. trichocarpa, P. balsamifera and their hybrids, including whole genome single nucleotide polymorphism (SNP) data for hundreds of individuals (Evans et al. 2014; Slavov et al. 2012; Geraldes et al. 2014), to detect introgressed regions at a fine scale using three target chromosomes. We also implemented functional and phenotypic tests to determine if introgressed regions are associated with adaptation, using extensive data on   phenotypic and transcriptome diversity in many of the same individuals grown in a common garden (McKown et al. 2103; McKown et al. 2014; Corea et al. in preparation).  Populus trichocarpa and P. balsamifera are sibling poplar species of the section Tacamahaca that diverged in allopatry rather recently (~76 Ka) during Pleistocene glaciations (Levsen et al. 2012); [see (Ismail et al. 2012) for an alternative - older - estimate]. They are major components of the forest ecosystems of northern North America and are economically important forest trees, being wood pulp sources and potential feedstock for cellulosic ethanol production (Jansson & Douglas 2007; Porth & El-Kassaby 2015). Despite their recent divergence and morphological similarity, with some minor differences in flower and fruit morphology, the species are ecologically divergent and adapted to strongly contrasting environments. P. trichocarpa is distributed throughout the western US and Canada, from northern California to southern Alaska, and is adapted to relatively humid, moist, and mild conditions west of the Rocky Mountains. P. balsamifera, on the other hand, is largely a boreal species distributed from Alaska to Newfoundland, with high frost tolerance and is adapted to environments where there can be huge annual temperature differences (-62˚C to 44˚C) and generally less annual precipitation (Richardson et al. 2014).  Recently, Geraldes et al. (2014) showed that introgression from P. balsamifera plays a role in shaping the geographically and climatically associated patterns of genetic variation of P. trichocarpa across much of its range. This admixture, geographically limited to contact zones located in Alaska, northwestern Canada and the Canadian Rockies (Figure 1) (Viereck & Foote 1970; Geraldes et al. 2014), may be driving adaptive processes if introgressed alleles are functionally different and linked to adaptive phenotypic traits. For example, introgression of P. balsamifera genes associated with faster growth rates that compensate for short growing seasons   at higher latitudes may allow admixed P. trichocarpa individuals to colonize new environments in northern and eastern regions. This could also be the case if introgressed P. balsamifera genes are associated with cold or drought tolerance (Soolanayakanahally et al. 2009).  Previous studies based on a 34K SNP genotyping array in ~500 P. trichocarpa individuals from the Pacific Northwest (Geraldes et al. 2013), found 88 genes with FST outlier SNPs (Geraldes et al. 2014) associated with 30 phenotypic traits (McKown et al. 2014) putatively underlying adaptive processes. Two unique sets of SNPs in candidate genes, located in chromosome 6 and chromosome 15 respectively, had FST values that were among the 10 highest - genome wide - and were strongly correlated with geoclimate variables (Geraldes et al. 2014). In addition, these SNPs were in high linkage disequilibrium (LD) with other candidate SNPs in the same chromosome, and/or had multiple trait associations based on a genome-wide association analysis (GWAS) (McKown et al. 2014). In this study, we tested if introgression from P. balsamifera was a source of any signals of local adaptation found in P. trichocarpa populations. In chromosome 6, adjacent genes FAR1 (Potri.006G020600) and FHY3 (Potri.006G020700), encoding transcription factors related to the far red light response, had SNPs with the highest FST genome wide, which are in high LD (Geraldes et al. 2014). In chromosome 15, a genomic region of ~600-kb showed strong patterns of structure and association with latitude, environmental variables (Geraldes et al. 2014) and phenology, biomass and ecophysiology traits (McKown et al. 2014). This ‘gene block’ had candidate SNPs in high pairwise LD, including those from a gene encoding a phenylpropanoid enzyme (COMT1, Potri.015G003100) and from transcription factors putatively involved in light and developmentally regulated gene expression (TTG1, Potri.015G002600; PRR5, Potri.015G002300; ANAC062, Potri.015G004100) (McKown et al. 2014). Interestingly, a paralog region of this genomic block found in chromosome 12, that was   produced by a whole genome duplication event in the Salicoid lineage (Tuskan et al. 2006), did not show signals of population structure or association with phenotypic traits, suggesting that these gene paralogs have followed different evolutionary trajectories.  Based on these results, we focused the current study on data obtained from population-wide genome resequencing of chromosomes 15 and 6 in P. trichocarpa and P. balsamifera, and of chromosome 12, which had a paralog block of the chromosome 15 candidate genes showing no signatures of selection. We (i) identified hot spots of introgression (i.e. regions that exhibited excess introgression relative to chromosomal averages) and tested if candidate regions for adaptation in P. trichocarpa have alleles introgressed from P. balsamifera, (ii) implemented genomic and gene ontology enrichment tests in introgressed regions to detect signals of selection and overrepresented biological terms respectively, (iii) analyzed gene expression levels to test if introgressed alleles could function differently from P. trichocarpa alleles, and (iv) compared phenotypes of admixed vs. pure P. trichocarpa individuals to explore the potential functional effects of introgressed alleles.  MATERIALS AND METHODS Samples  Populus trichocarpa accessions used in this study were collected by the British Columbia Ministry of Forests, Lands and Natural Resource Operations (MFLNRO) (Xie et al. 2009), and outplanted in a common garden at the University of British Columbia (McKown et al. 2013). These individuals comprised 28 “drainages” (i.e., topographic units separated by watershed barriers) spanning 14° in latitude (45.6°–59.6°) from throughout the species range. For P. balsamifera, we used accessions from 46 provenances throughout the species range obtained   from the Agriculture and Agri-Food Canada AgCanBaP collection (Soolanayakanahally et al. 2009). For local ancestry analysis in RASPberry (Wegmann et al. 2011), 50 reference individuals and 68 admixed individuals (36 P. trichocarpa individuals with P. balsamifera admixture, and 32 P. balsamifera individuals with P. trichocarpa admixture) were selected from the sympatric zone between P. trichocarpa and P. balsamifera as well as from allopatric populations (Figure 1). These 118 individuals were selected from a collection of 435 P. trichocarpa and 448 P. balsamifera genotypes, using a previous genome wide admixture analysis (see Supporting Information: Materials and Methods; Geraldes et. al., In preparation). Additional sample information and data generated in this and previous studies can be found in Table S1; Supporting Information.  Sequencing, read mapping and variant calling  Three different sample sets were used to call SNPs (Table S1; Supporting Information). For gene sequence analysis, SNPs were called for three genes (COMT1, PRR5, and TTG1) among 302 P. trichocarpa genotypes and for one gene (COMT1) among 243 P. balsamifera genotypes. For local ancestry analysis SNPs were called in three chromosomes (6, 12, 15) for 118 individuals (see above and Supporting Information: Materials and Methods). For phenotypic and gene expression analysis, 161 P. trichocarpa individuals were classified in genotypic categories using SNPs in a telomeric region of chromosome 15. We sequenced each of the genotypes at an expected coverage ranging from 15X to 30X using the Illumina HiSeq2000 platform. Short reads from the sequencing libraries were independently aligned to the P. trichocarpa version 3 (v3.0) genome using BWA (version 0.6.1-r104) with default parameters. We corrected mate pair metadata and marked duplicate molecules using the FixMateInformation and MarkDuplicates methods in the Picard package (http://picard.sourceforge.net). Reads present   in areas surrounding InDels were re-aligned using the IndelRealigner method from GATK (version v1.5-25-gf46f7d0). Next, we called SNPs and small indels independently using the UnifiedGenotyper method from GATK. SNPs were then filtered to exclude variants within 3bp of any identified variants, having a mapping quality less than 5, and a variant quality less than 30. Each SNP was annotated using SNPeff (Cingolani et al. 2012) with version 3 of P. trichocarpa genome. All raw sequencing data and alignment information have been deposited on SRA (Accession: PRJNA298917 ID: 298917).  Inference of local ancestry We estimated the probabilities for each of the possible ancestral configurations (P. balsamifera, P. trichocarpa or mixed ancestry) in every SNP across three chromosomes (6, 12 and 15), in 50 reference individuals and 68 admixed individuals using RASPberry, a software that implements a reliable Hidden Markov model (HMM) for admixture (Price et al. 2009).  For RASPberry analyses, SNPs with missing data in the parental genotypes were removed using Plink 1.07 (Purcell et al. 2007), the parental genotypes (50) were then phased with fastphase (Scheet & Stephens 2006) by creating the input files with FCGENE (Roshyara & Scholz 2014), and ancestries for each admixed individual were estimated in ADMIXTURE (Alexander et al. 2009). To select the parameters in RASPberry that best fit our data, we ran a number of parameter combinations - including time since admixture and recombination rate – using the 971k SNPs genome-wide data set (see Supporting Information: Materials and Methods), and selected the model with the highest log likelihood value (Table S2; Supporting Information). Using the 971k SNPs data set for this preliminary analysis allowed us to both estimate individual ancestries based on a genome-wide approach, and to run different parameter combinations relatively fast. For local ancestry analyses based on the whole sequence of   chromosome 6, 12 and 15, only SNP ancestries with probabilities >95% in one of the three categories were considered. The proportion of P. balsamifera ancestry in P. trichocarpa admixed individuals was calculated, for each SNP, by counting sites with P. balsamifera ancestry as two, and sites with mixed ancestry as one. We detected regions with unusually high levels of introgression in admixed P. trichocarpa individuals using a sliding window approach, and a significance cut-off of three standard deviations (SD) from the weighted mean across the three chromosomes based on SNP density per window. We used 100-kb, 500-kb and 1-Mb windows with steps of 20-kb, 100-kb and 200-kb respectively. The same procedure was implemented to estimate levels of P. trichocarpa ancestry in P. balsamifera admixed individuals. Characterization of introgressed regions and test of selection in pure species and admixed individuals First, we performed Gene Ontology enrichment analysis by comparing the list of introgressed genes with the list of all poplar genes (41,335) and the best annotated orthologs in Arabidopsis thaliana (based on Popgenie annotation; http://popgenie.org/), using the DAVID online database (Huang et al. 2008). Second, we estimated Tajima’s D values across chromosome 6, 12 and 15 for the 50 pure species individuals, using 50-kb windows in VCFtools v0.1.12b (Danecek et al. 2011). For introgressed regions with positive Tajima’s D values, we performed neighbor-joining analysis with 1000 bootstrap replicates using MEGA (Tamura et al. 2007). Third, we calculated levels of nucleotide diversity (π) for the pure species individuals across the three chromosomes using 50-kb windows in VCFtools v0.1.12b. Fourth, we estimated the average proportion of amino acid substitutions driven by directional selection (alpha) in pure species individuals for all introgressed regions including a section with the lowest nucleotide diversity (π) level, using Smith and Eyre-Walker’s alpha (Smith & Eyre-Walker 2002), and   generated confidence intervals by randomly selecting genes with replacement (bootstrapping) 1000 times in R v. 3.2.1 (R Development Core Team, http://www.r-project.org). Fifth, we estimated pairwise linkage disequilibrium (LD) as r2 in the pure species and a set of admixed individuals (see Supporting Information: Materials and Methods), 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) with expected values, E(r2), computed using the formula from Hill & Weir (1998) in an R script (http://www.r-project.org/).  Haplotype distribution of candidate genes for local adaptation For three candidate genes in chromosome 15 (PRR5, Potri.015G002300; TTG1, Potri.015G002600; COMT1, Potri.015G003100) that showed signatures of selection in previous studies (Table S3; Supporting Information) (McKown et al. 2014; Geraldes et al. 2014), we estimated the FST value per SNP using Arlequin 3.5.1.2 (Excoffier et al. 2005), in 302 accessions from 28 drainages across much of the P. trichocarpa’s range. These FST values were compared to P. trichocarpa’s whole genome average FST (mean=0.05; 99th percentile = 0.18) following Geraldes et al. (2014). Based on the coding regions of each gene, we inferred haplotypes using PHASE 2.1 (Stephens et al. 2001) and mapped the haplotype distributions. For the COMT1 gene, we also estimated allele frequencies across 46 P. balsamifera provenances (484 individuals). Finally, we analyzed a protein alignment of COMT2, a paralog of COMT1 encoded on chromosome 12, from P. balsamifera and P. trichocarpa genotypes, and a protein alignment of different homologous sequences retrieved from Phytozome (http://www.phytozome.net).       Gene expression and phenotypic analysis in admixed P. trichocarpa individuals For phenotypic analyses, we used data from McKown et al. (2013). Gene expression data were obtained from a population-wide RNAseq dataset based on a subset of the P. trichocarpa accessions from trees outplanted in the common garden at the University of British Columbia as described above (Xie et al. 2009; McKown et al. 2013). RNA was isolated from 385 developing xylem samples from 197 of the accessions, and from 389 samples of expanding leaves of defined developmental stage from a subset of 191 of the accessions. For both phenotypic and gene expression data, we focused on one introgressed region in chromosome 15 and on individuals from northern and central parts of the P. trichocarpa range. By excluding genotypes from southern locations, we aimed to remove the latitudinal variation inherent in some phenotypic traits of P. trichocarpa (McKown et al. 2013), and targeted locations close to the contact zone. We used published phenotypic data from 146 P. trichocarpa genotypes (McKown et al. 2013) and RNAseq data, as FPKM (Fragments Per Kilobase of transcript per Million mapped reads), from a subset (33) of those P. trichocarpa genotypes (Supporting Information: Materials and Methods, Table S1). Each of the 146 P. trichocarpa individuals were classified into one of three genotypic categories: homozygotes for P. balsamifera haplotypes (bb), heterozygotes (bt) and homozygotes for P. trichocarpa haplotypes (tt), based on phased genomic sequences of one introgressed region in chromosome 15 (Figure S1; Supporting Information). Nine phenotypic traits and expression levels of 134 genes were then compared among the three genotypic categories (bb, bt and tt) using ANOVAs with adjusted P-values with Bonferroni correction, and Tukey tests for multiple comparisons. For one candidate gene, PRR5, we used a gene co-expression network analysis for the xylem RNASeq dataset to identify the top 25 co-expressed genes, and compared the average mean-centered expression levels of these genes between the   three genotypic categories (bb, bt and tt) using an ANOVA. Finally, we validated the RNAseq data using quantitative reverse transcription PCR (qRT-PCR) in COMT1, a selected candidate gene (Table S4; Supporting Information).  RESULTS  Local ancestry analysis revealed three introgressed regions Using 186,376 SNPs across chromosome 6, 12 and 15, we detected three regions with P. balsamifera ancestry in admixed P. trichocarpa individuals (36): two in chromosome 15 and one in chromosome 6. These regions were above a significance cutoff of three Standard Deviations (SD) from the mean P. balsamifera ancestry (0.096, SD 0.066, weighted by SNP density), using 50-kb, 100-kb and 1-Mb window analysis. This was consistent with genome wide estimates based on a 971k SNP data set, where the mean P. balsamifera ancestry was 0.13 (SD 0.036). Across the remaining regions of P. trichocarpa chromosomes 6 and 15, and across the entire P. trichocarpa chromosome 12, levels of P. balsamifera ancestry were for the most part low, and did not surpass the significance cutoff. For downstream analyses, we used the results based on 100-kb windows (Figure 2), since this window size provided the best compromise between large numbers of windows with missing data (50-kb windows) and low resolution (1-Mb windows) (Figure S2; Supporting Information).  In chromosome 15, a large introgressed segment (880-kb) was located in a telomeric region (peak B in Figure 2), and included candidate genes PRR5, TTG1 and COMT1 as well as another 131 genes (Table 1; Table S3 and S5; Supporting Information). A second 580-kb introgressed region in chromosome 15 was located 13.34 Mb from the start of the chromosome and included 84 genes (peak C in Figure 2). In chromosome 6, a 580-kb introgressed region   comprised 67 genes and was located at 3.36 Mb from the start of the chromosome (peak A in Figure 2), downstream of candidate genes for adaptation (Table 1; Table S3 and S5; Supporting Information). Local ancestry analysis of P. balsamifera admixed individuals did not reveal introgression from P. trichocarpa (Figure S3; Supporting Information). Selection in pure P. balsamifera and P. trichocarpa The three introgressed regions revealed different patterns of Tajima’s D and alpha estimates in the parental genotypes. A section of introgressed region B (telomeric introgressed region of chromosome 15) that included candidate gene PRR5 revealed positive values of Tajima’s D in P. balsamifera but not in P. trichocarpa, with estimates greater than the neutral expectation (Figure 3). In P. balsamifera the first two 50-kb windows of this region showed Tajima’s D estimates above the 1% of the distribution (0 to 49-kb = 2.58; 50 to 99-kb = 3.18), and the following window showed Tajima’s D estimates above the 5% of the distribution (100 to 149-kb = 2.14) (Table S6; Supporting Information). A neighbour-joining (NJ) tree based on the first 880-kb of chromosome 15 revealed two haplotype clusters in P. balsamifera, both of which occur in populations from the northwestern and central parts of the species range (Figure S4; Supporting Information).  Region C in chromosome 15 also showed positive values of Tajima’s D higher than the 1% of the distribution, in both P. trichocarpa and P. balsamifera, but only in one 50-kb window (13.45 Mb to 13.50 Mb) (Figure 3), comprising three genes. Tajima’s D values in introgressed region C in chromosome 6 did not deviate from neutral expectations in either P. trichocarpa or P. balsamifera (Figure S5; Supporting Information).  Region B in chromosome 15 exhibited extended LD decay in both admixed and pure P. balsamifera individuals. In admixed individuals, average LD in this region did not decay below   2kb until past 10 kb, as it did in the second introgressed region (region C) and across the remainder of chromosome 15 (r2 decay to 0.2 at 2 kb and 5 kb respectively) (See Supporting Information and Figure S6). In pure P. trichocarpa and P. balsamifera LD decay also was extended in region B, with average LD not dropping below 2kb for 5 kb and 4 kb, respectively. LD decay in introgressed regions A and C in chromosomes 6 and 15, respectively, was similar to that in the chromosome-wide average (2 kb; Figure S6; Supporting Information). In pure P. balsamifera, a haplotype block at the start of chromosome 15 extended for 130 kb and was followed by a shorter block of 26 kb that included candidate genes PRR5 and TTG1 (Figure 4A). In pure P. trichocarpa, the haplotype block at the start of chromosome 15 extended for only 36 kb, and other blocks downstream were not longer than 8-kb (Figure 4B). In addition to positive values of Tajima’s D and relatively long haplotype blocks in pure P. balsamifera individuals, the first ~200 kb of chromosome 15 from region B (i.e. P. balsamifera introgressed region B in P. trichocarpa individuals) showed the highest levels of nucleotide diversity compared to levels across the three chromosomes examined (Figure S7; Supporting Information). Levels of nucleotide diversity (π) in the first 160 kb, comprising 25 genes including PRR5, were in the top 5% of the distribution in P. balsamifera. However the contiguous downstream region had the lowest P. balsamifera π values (lower than the bottom 5% of the distribution). Alpha estimates of this 110-kb region (from 183 kb to 280 kb in chromosome 15), comprising 14 genes including COMT1 and ANAC062, revealed signals of positive selection in 46% and 41% of all amino acid substitutions in P. trichocarpa and P. balsamifera respectively (Table 2). The alpha estimate for the entire telomeric introgressed region in chromosome 15 (region B) was not significantly different from zero, and neither was that for the introgressed region in chromosome 6 (region A). For the second introgressed region   in chromosome 15 (region C), synonymous and non-synonymous substitutions were not detected (Ds and Dn = 0) and alpha was undefined (Table 2). Haplotype distribution of candidate introgressed genes on P. trichocarpa  In COMT1 from P. trichocarpa, we identified 171 SNPs with a MAF (minor allele frequency) > 0.01, eight of which were in the coding region. The highest FST value in the coding region was for a synonymous SNP located in the first exon of the gene (amino acid position A84, FST = 0.3), and the second largest FST value was found in a nonsynonymous SNP (nsSNP, P287Q, FST =0.23) (Figure 5A), both of which were higher than the 99th percentile of the genome wide distribution (0.18) based on a previous analysis (Geraldes et al. 2014).  The P287Q polymorphism is located in the O-methyltransferase domain of the COMT1 enzyme, and the P287 variant was strictly conserved in all homologs including COMT2, a paralog of COMT1 encoded on Populus chromosome 12, and in COMT homologs from other species (Figure S8; Supporting Information). In P. trichocarpa, this site was polymorphic with the alternative Q287 variant occurring at a relatively low frequency (8.6%), and restricted to northern and interior populations (Figure 5B). In P. balsamifera, the Q287 allele was almost fixed (95%) and the alternative P287 variant only occurred in admixed individuals with P. trichocarpa and P. deltoides (Geraldes et. al., In preparation) (Figure 5C). These results support our finding of signals for positive selection in COMT1 and flanking genes (110-kb region from 170-kb to 280-kb in chromosome 15), and suggest that the rare Q287 COMT1 variant selected for in P. balsamifera, but not found in any other homologous COMT genes, introgressed to P. trichocarpa in regions close to the contact zone with P. balsamifera.    In TTG1 we found 20 SNPs with a MAF >0.01, five of which were in the coding region. The highest FST values in the coding region were for two sSNPs (L238-G/T, L323-A/C FST= 0.25), with T238/C323 alleles restricted to the north and interior (Figure S9-A, B; Supporting Information). In PRR5 we found 75 SNPs with a MAF >0.01, 12 of which were in the coding region and five of which were nsSNPs. The highest FST value in the coding region was found in nsSNP R396W (FST =0.24), where R396 was the most common allele and W396 was restricted to the north and interior with an allele frequency of 9.1% (Figure S9-C, D; Supporting Information). Evidence for adaptive introgression based on GO, gene expression and phenotypic analysis  GO term enrichment analysis of the three introgressed regions (region A in chromosome 6; region B and C in chromosome 15) revealed 11 GO terms and three protein groups overrepresented in region A in chromosome 6 (14 genes) and region B in chromosome 15 (25 genes) (Table S6; Supporting Information). From the total 39 genes associated with these biological processes, four genes - including PRR5 - were found in a genomic region showing an excess of intermediate-frequency alleles in P. balsamifera, and two genes, namely NAC147 and ANAC062, were located in a region with signals of positive selection in both P. balsamifera and P. trichocarpa (Table 1). The signals of selection and overrepresentation of genes that may play roles in adaptive traits (e.g. RNA processing, response to far red light, ATPase activity) further supports the potential of the telomeric region of chromosome 15 in adaptive introgression. In turn, genes in the second introgressed region (C) of chromosome 15 were not overrepresented in any of the 75,000 functional terms tested.  Based on gene expression analysis in the 880-kb introgressed region B, we identified seven genes - including TTG1 and COMT1 - out of 134 in which the level of expression was   significantly different in admixed individuals with P. balsamifera haplotypes (bb and bt), compared to P. trichocarpa genotypes (tt) in both xylem and leaf samples (Table S7; Supporting Information). TTG1 and COMT1 were among the most highly expressed genes and for both the highest expression was found in those homozygous for P. balsamifera haplotypes (bb), followed by heterozygotes (bt), with those homozygous for P. trichocarpa haplotypes (tt) showing the lowest expression (Figure 6). This variation in expression, especially pronounced for COMT1 and validated using qRT-PCR (Table S4, Figure S10; Supporting Information), suggests that introgressed alleles are functionally distinct at the level of gene expression.  In PRR5 we found that the mean-centered FPKM from the top 25 co-expressed genes was significantly lower in P. trichocarpa individuals homozygous for P. balsamifera PRR5 alleles (bb, W396W), compared to either individuals that were heterozygotes (bt, W396R), or homozygotes for P. trichocarpa PRR5 alleles (tt, R396R) (Figure S11; Supporting Information). Thus, the introgressed W396-PRR5 variant from P balsamifera may encode a functionally distinct protein with respect to its ability to regulate transcription of direct or indirect target genes in P. trichocarpa. Analyses of the phenotypic variation, based on a suite of nine ecophysiology, phenology and biomass traits, some measured in multiple years (Table S8; Supporting Information), also revealed significant differences between admixed individuals with P. balsamifera haplotypes (bb and bt) and P. trichocarpa genotypes (tt). Admixed individuals with P. balsamifera haplotypes (bb and bt) in the first 880-kb of chromosome 15 (region B, Figure 2) exhibited higher leaf chlorophyll content across two years (2009 and 2011, Figure 6A, B), and higher leaf nitrogen content in 2009 (Figure 6C). Leaf nitrogen content was not significantly different among   genotypes in 2010, probably due to a smaller sample size; in this year some trees set bud before measurements took place (McKown, personal communication).  DISCUSSION Our study revealed an approximately 880-kb genomic region in chromosome 15 with strong evidence for introgression from P. balsamifera into P. trichocarpa populations at higher frequencies than the genomic background, and provides evidence that this is an example of adaptive introgression. In contrast, a paralog block of duplicated genes on chromosome 12 showed no signs of introgression or signatures of selection, suggesting alternative evolutionary trajectories of these duplicated genes in Populus. Our analyses suggest that specific introgressed P. balsamifera alleles on chromosome 15 are under selection, are functionally distinct, and are correlated with the expression of adaptive traits in P. trichocarpa individuals that harbor them. Admixed individuals with these introgressed P. balsamifera haplotypes are restricted to northern and central areas of the geographical range of P. trichocarpa, and have been assigned to distinct climate clusters (Porth et al. 2015). Based on historical climate data, northern and north-central regions have significantly lower mean annual temperature (MAT: 4.2 ˚C), number of frost-free days (NFFD: 175 d), and mean annual precipitation (MAP: 744 mm) than coastal and southern regions (MAT: 9.5˚C, NFFD: 287 d, MAP 2805 mm) (Porth et al. 2015), suggesting potential niche differentiation between populations with and without the introgressed region.  A telomeric region on chromosome 15 is a hot spot for introgression Local ancestry analysis revealed three introgressed regions, one of which was located in a telomeric region of chromosome 15 (region B), showed high LD levels and signals of selection in both pure species, and included several candidate genes for local adaption identified by   previous association studies (McKown et al. 2014) and FST outlier tests (Geraldes et al. 2014) (Table S3; Supporting Information). To explain these results we propose two scenarios: recent hybridization and adaptive introgression, which are not mutually exclusive.  Region B in chromosome 15 was the largest among the three introgressed regions and had LD levels higher than the genomic background, which may indicate recent admixture with insufficient time for recombination to have reduced LD within the introgressed region. The micro-evolutionary processes at work in the hybrid zone may not – or not yet – have impacted adjacent or allopatric populations of the hybridizing species (Harrison & Larson 2014), also explaining the low frequencies of introgressed alleles in candidate genes (e.g. 8.6% COMT1-Q287, 9.1% PRR5-W396) in P. trichocarpa, and the relatively high levels of divergence still present in parental linages (Figure S4; Supporting Information). However in pure P. balsamifera, the presence of haplotype blocks in the telomeric region of chromosome 15 (first 150-kb), the excess of intermediate-frequency alleles and the segregation of two distinct haplotypes, all of which could be signatures of balancing selection (Vitti et al. 2013), lead us to an alternative scenario: two types of haplotype blocks selected for in pure P. balsamifera introgressed as a modular, or cassette-like block of genes into P. trichocarpa, and these now underlie adaptive processes in the P. trichocarpa admixed individuals as well as in the P. balsamifera donor species.  In line with the latter adaptive introgression scenario, the telomeric region of chromosome 15: (i) is enriched for genes that may play crucial roles for survival and adaptation, such as those related to response to far red light, RNA processing and ATPase activity, (ii) contains a section (from 200 kb to 280 kb) showing signals of positive selection in both pure P.   balsamifera and P. trichocarpa, and (iii) includes introgressed alleles affecting P. trichocarpa phenotypes according to functional as well as phenotypic analyses.  Evidence that introgressed P. balsamifera alleles are functionally different from P. trichocarpa variants The introgressed region B in chromosome 15 is enriched for 11 GO terms and three protein groups with overrepresentation of genes that may play crucial roles for survival and adaptation, such as those related to response to far red light, RNA processing and ATPase activity. Four of the genes associated with these biological processes, including PRR5, were found in a section of the introgressed region that showed signals of excess intermediate-frequency alleles in P. balsamifera, and two other genes (NAC147 and ANAC062) were located in a region with signals of positive selection in both P. balsamifera and P. trichocarpa. A third candidate gene that showed signals of purifying selection in both pure P. trichocarpa and P. balsamifera genotypes is COMT1, which encodes a key phenylpropanoid enzyme. The functions of candidate genes PRR5 and COMT1, and evidence for functional differentiation of introgressed alleles of PRR5 and COMT1, are discussed below. Candidate gene PRR5. The Populus PSEUDORESPONSE REGULATOR5 (PRR5) in the introgressed region encodes a transcriptional regulator that is an important component of the circadian clock mechanism, based on studies in Arabidopsis (Nakamichi et al. 2010; Wang et al. 2010). In Populus, PRR5 is upregulated at the onset of short days and it may play a crucial role in the timing of the onset of bud dormancy in P. trichocarpa (Ruttink et al. 2007; Ko et al. 2011). Furthermore, a transcriptomic analysis of an Arabidopsis prr9, prr7, prr5 triple mutant suggested that these pseudo-response regulators negatively affect the expression of genes encoding enzymes associated with chlorophyll biosynthetic pathways (Fukushima et al. 2009).    Introgressed PRR5 P. balsamifera variants have a nsSNP W396 substitution located between the pseudoreceiver domain and the CCT motif, in a highly conserved 44-amino acid region shown to be essential for PRR5 transcription repressor activity in Arabidopsis (Nakamichi et al. 2010). This position in P. trichocarpa alleles, as in other PRR genes from other species including Arabidopsis, is usually occupied by an amino acid with a positively charged R-group (R or H). It is possible that the P. balsamifera W396 PRR5 allele, with a nonpolar amino acid at that site, represses target genes in a different manner compared to common P. trichocarpa alleles, which instead have a polar amino acid at that site (R396). In P. trichocarpa, we found that the levels of expression of the top 25 genes co-expressed with PRR5 are significantly lower in P. trichocarpa individuals homozygotes for P. balsamifera PRR5 alleles (WW) compared to either individuals that were heterozygotes (WR) or homozygotes for P. trichocarpa PRR5 alleles (RR) (Figure S11; Supporting Information). This finding suggests that the introgressed W396 protein variant is functionally distinct, since it appears to differ in its transcriptional regulatory activity in the clock-regulated gene network. Future functional studies will test the hypothesis that the PRR5 protein variants have different biochemical and/or physiological functions.  Analysis of phenotype partitioning in admixed P. trichocarpa individuals revealed that those with P. balsamifera haplotypes on the telomeric region of chromosome 15, including the PRR5 W396 allele, showed higher chlorophyll content and higher leaf nitrogen content compared to those without P. balsamifera alleles (Figure 6). Previous studies in Picea abies (Norway spruce) (Oleksyn et al. 1998) and P. balsamifera (Soolanayakanahally et al. 2009) showed that higher chlorophyll and leaf nitrogen content are associated with higher photosynthetic rates, and in P. balsamifera these traits were also correlated with faster growth and higher carbon acquisition. In P. trichocarpa (McKown et al. 2013) and P. balsamifera   (Soolanayakanahally et al. 2009) photosynthetic rates are also positively correlated with latitude; where faster growth and higher carbon acquisition may counteract shorter growth seasons at higher latitudes. Our analysis of the genetic effects of introgressed balsam alleles on P. trichocarpa phenotype (higher chlorophyll and leaf nitrogen content) suggests that admixed individuals may grow and acquire carbon faster than pure P. trichocarpa individuals from the same provenances. Future glasshouse studies will test this hypothesis in an effort to elucidate the importance of this phenotype in P. trichocarpa northern populations.  Candidate gene COMT1. A second candidate gene that showed signals of purifying selection in both pure P. trichocarpa and P. balsamifera genotypes is COMT1 (CAFFEIC ACID 3-O-METHYLTRANSFERASE 1), which encodes a key phenylpropanoid enzyme required for the biosynthesis of sinapyl alcohol and metabolites derived from sinapyl alcohol, and that could be involved in lignification and/or pathogen defense (Barakat et al. 2011). In COMT1, we also found evidence for functionally distinct P. balsamifera COMT1 alleles based on gene expression differences in both leaf and xylem (Figure 6). COMT1 expression in P. trichocarpa admixed individuals homozygous for P. balsamifera introgressed alleles (bb) is high, in tt individuals low, and in bt individuals intermediate, suggesting that P. balsamifera alleles are functionally different from P. trichocarpa alleles and have the potential to affect the phenotype of admixed individuals. In COMT1 we found one SNP in the promoter region in tight linkage with a nsSNP (P287Q) that differentiates P. balsamifera from P. trichocarpa COMT1 alleles (Figure S12; Supporting Information), and that could potentially be a cis-regulatory element causing the difference in expression.  The introgressed COMT1 Q287 allele is restricted to northern P. trichocarpa populations in close proximity to contact zones (Figure 5), but is nearly fixed and under selection in P.   balsamifera (Figure 5). The unusual P. balsamifera COMT1 Q287 variant - P287 was strictly conserved in all COMT homologs; Figure S8; Supporting Information - may affect the enzyme activity, with a substitution of a nonpolar amino acid (proline-P) for a polar amino acid (glutamine-Q), in a site in close proximity to conserved catalytic histidine (H) and glutamic acid (E) residues (Zubieta et al. 2002) (Figure S13; Supporting Information). This could result in a competitive disadvantage to individuals with introgressed Q287 alleles at lower latitudes, where both temperature and precipitation are higher. It is also possible that Q287-COMT1 variants have lower enzyme efficacy and that an increase in gene expression is needed to overcome this change in enzyme activity. These results suggest that functional differences between P. balsamifera and P. trichocarpa COMT1 alleles may contribute to differences in fitness in specific environments.  Overall, our results suggest that PRR5 and COMT1 are good candidate genes to explain the signals of selection found in the telomeric introgressed region B of chromosome 15, consistent with the introduction of modular, or cassette-like variation into P. trichocarpa, where multiple linked introgressed alleles such as PRR5 R396W and COMT P287Q are associated with adaptive traits (Abbott et al. 2013). However, since this region comprises 134 genes, a plausible alternative scenario is that PRR5, COMT1 and other candidate genes are hitchhiking and the actual targets (or target) of selection remain to be uncovered. Future work will be required to distinguish between these possibilities.  Introgression and functional divergence in paralogous genes While genes within block B on the chromosome 15 telomeric region are under selection, are associated with adaptation, and have apparently adaptively introgressed into northern and central P. trichocarpa populations (this study; Geraldes et al. 2014; McKown et al. 2014), a highly syntenic block of paralogous duplicated genes on chromosome 12, derived from the   whole genome duplication event in the Salicoid lineage (Tuskan et al. 2006), showed neither evidence for introgression nor signatures of selection. This is consistent with the lack of signatures of adaptation for the chromosome 12 paralogs in previous studies (Geraldes et al. 2014; McKown et al. 2014). Interestingly, chromosome 12 paralogs - such as TTG2 and COMT2 - and candidate genes in chromosome 15 - such as TTG1 and COMT1 - have different expression patterns (Sjödin et al. 2009; Hefer et al. 2015). For example, while the expression pattern of the COMT2 paralog on chromosome 12 clearly implicates this gene in developmental lignification (Barakat et al. 2011), the chromosome 15 paralog COMT1 is not highly expressed in developing xylem, but is strongly induced by herbivory (Barakat et al. 2011). These data suggest potential sub- and/or neo-functionalization of paralogs on chromosomes 15 and 12, which may have facilitated the co-opting of certain chromosome 15 paralogs for new roles in adaptation. A plausible scenario is that further microevolution of chromosome 15 paralogs such as COMT1, PRR5, and TTG1 contributed to local adaptation in P. balsamifera, and that such alleles subsequently introgressed into P. trichocarpa populations, adapting them to transitional environments at the northern and north-central extremes of this species’ range.   Acknowledgements This work was supported by the Genome Canada Large-Scale Applied Research Program (POPCAN, project 168BIO), funds to QCBC and CJD, by a Natural Sciences and Engineering Research Council of Canada Discovery Grant to CJD (RGPIN 36485-12), and by grants of the Swiss National Science Foundation (SNF) to CL. AS-G was partially supported by a ThinkSwiss Fellowship and the Biodiversity Research Integrative Training & Education (BRITE) program. We thank Michael Friedmann (UBC) for assistance with project management; and Armando   Geraldes, Arnaud Capron, Athena McKown, Felix Martinez-Nuñez and Robert Guy (UBC), and Daniel Wegmann (U Fribourg) for assistance and discussions. References Abadie P, Roussel G, Dencausse B, et al (2012) Strength, diversity and plasticity of postmating reproductive barriers between two hybridizing oak species (Quercus robur L. and Quercus petraea (Matt) Liebl.). Journal of Evolutionary Biology, 25, 157-173. 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Zubieta C, Kota P, Ferrer J, Dixon RA, Noel JP (2002) Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-Methyltransferase. The Plant Cell, 14, 1265-1277.   Data Accessibility   All raw whole genome sequencing data and alignment information has been deposited on SRA (Accession: PRJNA276056; ID: 276056) available at this link: http://www.ncbi.nlm.nih.gov/sra/?term=PRJNA276056. All RNA-seq data has been deposited in the NCBI under Bioproject ID 300564, available at this link: http://www.ncbi.nlm.nih.gov/bioproject/300564.The input files and data used in all the analyses have been archive in dryad: doi:10.5061/dryad.0817m (see Supporting Information: Materials and Methods). Author Contributions AS-G, CJD and CL designed the study, with input from QCBC. AS-G performed the research and analyzed data with assistance from CC (RASPberry analysis) and OC (gene co-expression network analysis). CH performed SNP calling and RNA-seq bioinformatics analyses. CJD, QCBQ, and CL provided funding. All authors contributed to writing the manuscript and approved the final version.     Tables  Table 1. List of three introgressed regions (A, B, C – see Figure 2) from P. balsamifera in P. trichocarpa in chromosome (Chr) 6 and 15. Genes in region B with signals of selection, and associated with enriched GO terms (11) and protein groups (3) are shown.  Chr Region Genomic coordinates # of Genes Genes under selection and associated with enriched GO terms   start end  6 A 3360000 3940000 67  15 B 0 880000 134 Potri.015G000200 §      Potri.015G001200 §      Potri.015G002200 §      Potri.015G002300 §      Potri.015G002900 ¶      Potri.015G004100 ¶ 15 C 13340000 13920000 84   § Genes showing relatively high levels of Tajima’s D. ¶ Genes showing signals of positive selection (alpha).    Table 2. Alpha estimates for three introgressed P. balsamifera regions in P. trichocarpa, one in chromosome (Chr) 06 (region A) and two in chromosome 15 (B and C).   Chr Region Species # of Genes alpha CI 6 A P. balsamifera 67 0.16 -0.6286   P. trichocarpa 67 0.16 -0.6271 15 B P. balsamifera 128 -0.47 -1.3095   P. trichocarpa 128 -0.38 -1.29 15 B† P. balsamifera 14 0.41 0.1285 - 2.5087*   P. trichocarpa 14 0.46 0.1625 - 2.2363* 15 C P. balsamifera 83 NA NA     P. trichocarpa 83 NA NA CI: Bootstrap confidence intervals. † Genomic region with lowest levels of nucleotide diversity (p) in P. balsamifera (< the bottom 5% of the distribution). * alpha estimate significantly different from zero. NA: No polymorphism data; alpha is undefined.     Figures Figures  Figure 1. Geographic distribution of admixed and reference individuals used in local ancestry analysis across the contact zones between P. trichocarpa and P. balsamifera. Ranges of P. trichocarpa and P. balsamifera are shown in red and blue, respectively (Little 1971).        Figure 2. Proportion of P. balsamifera ancestry in admixed P. trichocarpa individuals across chromosomes 6, 12, and 15 based on sliding window analysis (size: 100-kb, step: 20-kb). Introgressed regions – peaks A, B, C -have P. balsamifera ancestry higher than 3 standard deviations from the weighted mean across chromosomes 6, 12 and 15 based on SNP density per window (broken line). Asterisks represent the chromosomal position of candidate genes: FAR1 (Potri.006G020600) and FHY3 (Potri.006G020700) in chromosome 6, and COMT1 (Potri.015G003100), TTG1 (Potri.015G002600), PRR5 (Potri.015G002300) ANAC062 (Potri.015G004100) in chromosome 15. In chromosome 12, the asterisk represents the position of the COMT1 paralog, COMT2 (Potri.012G006400).      Figure 3. Tajima’s D analysis across chromosome 15 in Populus balsamifera and P. trichocarpa individuals calculated in 50-kb windows. (Top) Tajima’s D values across chromosome 15 are represented by blue and red continuous lines for P. balsamifera and P. trichocarpa respectively, and introgressed regions B and C are shown (see Figure 2). Values representing the top 95% of the distribution are shown in blue and red dashed lines for P. balsamifera and P. trichocarpa respectively; (Bottom) Tajima’s D values in introgressed regions B of chromosome 15 (telomeric region from 0 to 880-kb) with straight solid blue and red lines representing the top 99% of the distribution for P. balsamifera and P. trichocarpa respectively. The Asterisk represents the chromosomal position of candidate gene PRR5 (Potri.015G002300).      Figure 4. Linkage disequilibrium (LD) plot of the first 200-kb of chromosome 15 introgressed region in pure P. trichocarpa (B) and P. balsamifera (A). Red areas represent pairs of SNPs with high levels of LD (D’=1, LOD ≥2) and blue areas represent pairs of SNPs with LD comparisons with a low estimation confidence (LOD < 2). Dark triangles represent haplotype blocks based on Gabriel et al. (2002). In P. balsamifera a haplotype block at the start of chromosome 15 extends 130 -kb but in P. trichocarpa it extends to only 38-kb.     Figure 5. COMT1 alleles and geographic distribution in P. trichocarpa and P. balsamifera populations. (A) Gene model of COMT1 with arrows depicting SNPs with the top Fst values in the coding region, which were higher than the 99th percentile of the genome wide distribution (0.18) based on a previous analysis (Geraldes et al. 2014). The green arrow shows nsSNP P287Q (FST=0.23), the yellow arrow represents sSNP A84 (FST= 0.3) and black arrows depict SNPs in the non-coding region (5’UTR and introns). (B) Geographic distribution of COMT1 haplotypes from 28 drainages in Populus trichocarpa, based on the nsSNPs with the highest Fst value (P287Q). (C) Geographic distribution of COMT1 haplotypes from 46 drainages in P. balsamifera. P. balsamifera individuals with P287 COMT1 alleles (easternmost population) are admixed with P. deltoides (Geraldes et. al., In preparation)      Figure 6. COMT1 (A) and TTG1 (B) gene expression levels in leaf and xylem of P. trichocarpa individuals with different haplotypes for introgressed region B from P. balsamifera. Gene expression is presented as FPMK (Fragments Per Kilobase of transcript per Million mapped reads) based on RNAseq data. Genotypes are based on the first 880-kb of chromosome 15 (see Figure 2): bb, homozygotes for the P. balsamifera introgressed region B [six samples from three genotypes]; bt, individuals heterozygous for the introgressed region [10 samples from five genotypes]; tt, individuals homozygous for P. trichocarpa haplotypes in the same region [65 samples from 24 genotypes]. The standard error (SE) within each genotypic class (bb, bt, tt) is represented by the bars. Shared letters above columns indicate that the average gene expression levels were not significantly different between those genotypes (p<0.05).       Figure 7. Boxplot diagrams depicting leaf chlorophyll content and leaf nitrogen content in P. trichocarpa individuals from northern and interior locations, with different haplotypes for introgressed region B from P. balsamifera (first 880-kb of chromosome 15, see Figure 2). bb, homozygotes for the P. balsamifera introgressed region B; bt, individuals heterozygous for the introgressed region; tt, individuals homozygous for P. trichocarpa haplotypes in the same region. (A) leaf chlorophyll content measured in 2009 [sample size: tt = 73, bt = 20, bb = 7], (B) leaf chlorophyll content measured in 2011 [tt = 47, bt = 9, bb = 3], (C) leaf nitrogen content measured in 2011 [tt = 100, bt = 30, bb = 8]. Each box shows the lower quartile, median and upper quartile values and the whiskers show the range of the phenotypic variation. Chlorophyll   content units are in Chlorophyll Concentration Index (CCI), and shared letters above columns indicate when differences between genotypes were not significant (p<0.05). Data from (McKown et al. 2013).  Supporting information: Figures and Tables List of Supporting Figures Figure S1. Neighbor-Joining (NJ) trees of 25 pure P. balsamifera, 25 pure P. trichocarpa, and 146 additional P. trichocarpa individuals from phased SNPs of an introgressed region of chromosome 15 Figure S2.  Proportion of P. balsamifera ancestry in admixed P. trichocarpa individuals analyzed in three sliding window sizes Figure S3. Proportion of P. trichocarpa ancestry in admixed P. balsamifera individuals across chromosomes 6, 12, and 15 Figure S4. Neighbor-Joining (NJ) tree of parental linages based on the first 880 kb of chromosome 15. Figure S5. Tajima’s D analysis in pure P. balsamifera and P. trichocarpa individuals in chromosome 6 and 12 based on 50-kb windows Figure S6. Linkage disequilibrium (LD) decay with distance Figure S7. Nucleotide diversity (π) levels across the first 1 MB of chromosome 15 Figure S8. Partial protein alignment of different COMT1 homologs. Figure S9.  TTG1 and PRR5 alleles and geographic distribution of haplotypes in P. trichocarpa populations Figure S10.  Relative gene expression (based on 2–ΔCT) of COMT1 among P. trichocarpa individuals with different COMT1 alleles  Figure S11. Box plot of the mean-centered FPKM values for the expression of the top 25 genes co-expressed with PRR5 in xylem.    Figure S12. LD plot of COMT1 in individuals from northern and central parts of P. trichocarpa’s range. Figure S13. Three-dimensional protein model of P. trichocarpa COMT1 based on template 1KYW.    Figure S1. Neighbor-Joining (NJ) trees of 25 pure P. balsamifera, 25 pure P. trichocarpa, and 146 additional P. trichocarpa individuals from phased SNPs of an introgressed region of chromosome 15. (A) Tree based on the first 880 kb chromosome 15.  (B) Tree based on the first 300 kb of chromosome 15.  Pure P. trichocarpa accessions are shown by filled red triangles, pure P. balsamifera accessions are shown by filled blue triangles and circles and additional P. trichocarpa individuals accessions from northern and central regions of the range are shown by open blue or red triangles. The cluster of P. balsamifera haplotypes (open and filled blue triangles) had strong support in (A) and (B). The accession codes for haplotypes from three representative individuals are shown: one homozygote (bb) for P. balsamifera haplotypes (kim166), one heterozygote (bt; als14) and one homozygote (tt) for P. trichocarpa haplotypes (ame133). The NJ analyses were conducted in MEGA6. Since we did not have information about the local ancestry patterns for all the 146 genotypes (in RASPberry we only included 36 P. trichocarpa admixed individuals), we used the phased introgressed region of chromosome 15 from all P. trichocarpa genotypes (146) as well as from the reference panel of individuals and implemented a NJ tree analysis - 1000 bootstrap replicates in MEGA (Tamura et al. 2007). These NJ trees, based on either the entire 880-kb chromosome 15 region B (A) or a smaller 300-kb portion at the start of the B region (B), revealed a well-defined cluster (bootstrap values: 80 and 99 based on 880-kb and 300 kb regions respectively) where haplotypes from pure P. balsamifera individuals grouped with haplotypes from admixed P. trichocarpa individuals. Based on these trees we identified eight genotypes homozygous for P. balsamifera haplotypes (bb: both haplotypes of the individual were found inside the P. balsamifera cluster), 32 heterozygous genotypes (bt: only one haplotype was found inside the P. balsamifera cluster) and 104 genotypes homozygous for P. trichocarpa haplotypes (tt: none of the haplotypes were inside the P. balsamifera cluster).      Figure S2.  Proportion of P. balsamifera ancestry in admixed P. trichocarpa individuals analyzed in three sliding window sizes. P. balsamifera ancestry across (blue lines) chromosome 6, 12 and 15 is shown in three sliding window analyses (sizes: 100kb, 500kb and 1Mb with steps: 20kb, 100kb, 200kb respectively). Grey broken lines represent SNP density per window.     Figure S3. Proportion of P. trichocarpa ancestry in admixed P. balsamifera individuals across chromosomes 6, 12, and 15. Solid line: admixture in chromosomes 6, 12, and 15 based on sliding window analysis (size: 100kb, step: 20kb). Broken line: 3 standard deviations from the weighted mean across chromosomes 6, 12 and 15 based on SNP density per window.        Figure S4. Neighbor-Joining (NJ) tree of parental linages based on the first 880 kb of chromosome 15. 25 P. trichocarpa accessions are shown in red and 25 P. balsamifera are shown in blue and purple. Branch lengths represent genetic distances using the p-distance method. For P. balsamifera, blue represents haplotypes from populations in the northwestern parts of the range and purple represents haplotypes from central populations.  The NJ analysis was conducted in MEGA6.      Figure S5. Tajima’s D analysis in pure P. balsamifera and P. trichocarpa individuals in chromosome 6 and 12 based on 50-kb windows. P. balsamifera and P. trichocarpa Tajima’s D values are represented by blue and red continuous lines respectively. The introgressed region in chromosome 6 is depicted by letter A; the paralog region of region B of chromosome 15 in chromosome 12 is represented by an asterisk (*) (see Figure 2 for details). Tajima’s D values representing the 95% of the distribution are shown in blue and red broken lines for P. balsamifera and P. trichocarpa respectively.      Figure S6.Top: Linkage disequilibrium (LD) decay with distance in P. balsamifera and P. trichocarpa based on single-nucleotide polymorphisms (SNPs) across three chromosomes (6, 12, 15 – dotted line) and three introgressed regions (region A in chromosome 6 – purple, region B in chromosome 15 – blue, region C in chromosome 15 – cyan). Bottom: LD decay with distance in a set of admixed P. trichocarpa individuals (see Supplementary M&M) based on SNPs across chromosomes (15 – dotted line) and two introgressed regions in chromosome 15 (region B– blue, region C– cyan).Admixed P. trichocarpa         Figure S7. Nucleotide diversity (π) levels across the first 1 MB of chromosome 15. π was assessed in sliding windows (size: 100kb, step: 20kb) in pure P. balsamifera (blue continuous line) and pure P. trichocarpa (red continuous line) individuals. In admixed P. trichocarpa individuals, the first 880kb of chromosome 15 showed signals of introgression from P. balsamifera. Nucleotide diversity values representing the 95% and 5% of the distribution are shown in blue and red broken lines for P. balsamifera and P. trichocarpa respectively.                                >Populus_trichocarpa_COMT2       SVP-KADAVFMKWICHDWSDAHCLKFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_trichocarpa_COMT1       SVP-QADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_balsamifera_COMT1       SVP-NADAVFMKWICHDWSDEHCLRFLKNCYDALQENGKVILVECILPVAPD--TSLATK >Populus_angustifolia_COMT1      SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_cathayana_COMT1         SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_deltoides_COMT1         SVP-QADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_fremontii_COMT1         SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_heterophylla_COMT1      SVP-QADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_koreana_COMT1           SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_lasiandraa_COMT1        SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_maximowiczii_COMT1      SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_szechuanica_COMT1       SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_tristisa_COMT1          SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Populus_ussuriensis_COMT1       SVP-KADAVFMKWICHDWSDEHCLRFLKNCYDALPENGKVILVECILPVAPD--TSLATK >Medicago_savatia_COMT           SIP-KADAVFMKWICHDWSDEHCLKFLKNCYEALPDNGKVIVAECILPVAPD--SSLATK >Arabidopsis_thaliana_COMT       SVP-KGDAIFMKWICHDWSDEHCVKFLKNCYESLPEDGKVILAECILPETPD--SSLSTK >Arabidopsis_thaliana_IGMT2      DVP-TGDAMILKRILHDWTDEDCVKILKNCWKSLPENGKVVVIELVTPDEAEN-GDINAN >Liquidambar_styraciflua_COMT    SVP-KGDAIFMKWICHDWSDEHCLKFLKKCYEALPTNGKVILAECILPVAPD--ASLPTK >Nicotiana_tabacum_COMT          SVP-KADAIFMKWICHDWSDEHCLKFLKNCYEALPANGKVIIAECILPEAPD--TSLATK >Zea_mays_COMT                   SVP-AGDAILMKWILHDWSDAHCATLLKNCYDALPENGKVIVVECVLPVNTE--ATPKAQ >Lolium_perenne_COMT             EVP-SGDTILMKWILHDWSDQHCATLLKNCYDALPAHGKVVLVQCILPVNPE--ANPSSQ >Clarkia_breweri_IEMT            GVP-KGDAIFIKWICHDWSDEHCLKLLKNCYAALPDHGKVIVAEYILPPSPD--PSIATK >Chrysosplenium_americanum_OMT2  SVP-KGDAIFMKWICHDWSDEHCLKLLKNCYDALPNNGKVILAECILPEVPD--SSLATK >Zinnia_elegans_COMT_ZINEL       SVP-KGDAIFMKWILHDWSDAHCLQVLKNCYKSLPENGKVIVAECILPEAPD--TTPATQ >Coptis_japonica_SMT             GVP-NAQNILLKWVLHDWDDDRSIKILKNCWKALPENGTVIVIEFVLPQVLG--NNAESF >Pinus_radiata_O24287            TVP-TGDAIFMKWIMHDWNDEDCIKILKNCRKAIPDTGKVIIVDVVLDADQGDNTDKKRK   Consensus/80%                    *VP.ptDAlFMKWIhHDWSDEHCl+bLKNCYcALPpsGKVIlsEsILP.sP-..s*bt*c  Figure S8. Partial protein alignment of different COMT1 homologs.  All P. data were obtained from whole genome resequencing of the species indicated (Cronk et al., unpublished); other sequences are from Phytozome (http://www.phytozome.net). The alignment figure was created using CHROMA (http://www.llew.org.uk/chroma/). The star indicates the position of the Q287 variant in the P. balsamifera COMT1 sequence, a position occupied by a P287 in all other COMT sequences analyzed (indicted by red P in the consensus amino acid sequence). The arrows represent theconserved catalytic histidine (H) and glutamic acid (E) residues identified by Zubieta et al. (2002).                 Figure S9.  TTG1 and PRR5  alleles and geographic distribution of haplotypes in P. trichocarpa populations. Gene models and of TTG1 (A) and PRR5 (C) are shown with arrows depicting SNPs with the highest FST values across each whole gene sequence (top six). Yellow arrows represent synonymous SNPs, green arrows represent non \synonymous SNPs and black arrows depict SNPs in the non-coding region (UTRs and introns). Geographic distribution of TTG1 (B) and PRR5 (D) haplotypes from 28 drainages in P. trichocarpa, based on the SNPs with the highest FST values in the coding region. In TTG1 (B) the highest FST values in the coding region was for two sSNP (L238, L323, FST= 0.25) with alleles restricted to the north and interior. In PRR5 (D), the highest FST value in the coding region was for one nsSNP (R396W, FST=0.24).               Figure S10.  Relative gene expression (based on 2–ΔCT) of COMT1 among P. trichocarpa individuals with different COMT1 alleles          Figure S11. Box plot of the mean-centered FPKM values for the expression of the top 25 genes co-expressed with PRR5 in xylem.  Genes had Pearson coexpression coefficients of  > 0.66 with PRR5 across 389 samples. Data is from P. trichocarpa individuals homozygotes for P. balsamifera PRR5 alleles (WW), heterozygotes (WR) and homozygotes for P. trichocarpa PRR5 alleles (RR). ANOVA revealed a significantly lower expression in WW individuals compared to either WR or RR individuals (p<0.05). Top 25 genes coexpressed with PRR5 (PCC > 0.66): Potri.001G205800; Potri.002G178200; Potri.003G194000; Potri.004G177000; Potri.004G217600; Potri.006G004700; Potri.006G067700; Potri.006G143300; Potri.006G184800; Potri.006G279900; Potri.007G050100; Potri.008G004300; Potri.008G077100; Potri.008G206300; Potri.009G015000; Potri.009G137200; Potri.010G086700; Potri.011G043200; Potri.011G082600; Potri.012G003700; Potri.012G005900; Potri.012G082600; Potri.013G046300; Potri.018G107000; Potri.018G129700.       Figure S12. LD plot of COMT1 in individuals from northern and central parts of P. trichocarpa’s range. Red diamonds represent pairs of SNPs with high levels of LD (D’=1, LOD ≥2). Green triangle represents nsSNP P287Q; purple triangle represent site 240301 (P. trichocarpa version 3 - v3.0 genome) in the intergenic region upstream of the 5’UTR region. Asterisk (*) represent LD between these two sites (D’=1; r2=1). Red areas represent pairs of SNPs with high levels of LD (D’=1, LOD ≥2) and blue areas representing pairs of SNPs with LD comparisons with a low estimation confidence (LOD < 2). Dark triangles represent haplotype blocks based on Gabriel et al. (2002).     Figure S13. Three-dimensional protein model of P. trichocarpa COMT1 based on template 1KYW. The homology model (in blue) was constructed using UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) interface and Modeller based on template 1KYW (in beige) (Zubieta et al. 2002).   References: Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution, 24, 1596-1599. Zubieta C, Kota P, Ferrer J, Dixon RA, Noel JP (2002) Structural Basis for the Modulation of Lignin Monomer Methylation by Caffeic Acid/5-Hydroxyferulic Acid 3/5-O-Methyltransferase. The Plant Cell, 14, 1265-1277.            List of Supporting Tables  Table S1. List of P. trichocarpa and P. balsamifera accessions used in this study and biogeographical data (latitude, longitude, elevation). Data generated by this study is highlighted in orange (i.e.SNPs for local ancestry analysis, RASPberry; and gene sequence analysis. See M&M and Supplementary Figure 2). Data previously published is highlighted in blue (i.e. phenotypic data, McKown et at. 2013, DOI: 10.1111/nph.12601, S2 in nph12601-sup-0002-TablesS1-S8.xlsx) and that in preparation is highlighted in purple (RNA-seq, O. Corea, S. Biswas et al., preparation; PCA and preliminary RASPberry analysis, Geraldes et al in preparation)  Table S2. Parameters for the RASPberry model with the highest log likelihood value, based on a whole genome SNP data set (see supplementary M&M) in 25 pure P. balsamifera, 25 pure P. trichocarpa and 68 admixed individuals.  Table S3. Candidate genes for local adaptation across P. trichocarpa’s range, in chromosome 6 and 15 based on FST outlier tests and/or association analysis with environmental variables and phenotypic traits (Geraldes et al. 2014; McKnown et al. 2014), and using a 34k SNP chip.  Table S4. Quantitive reverse transcription PCR (qTt-PCR) to test the levels of expression of  COMT1 genes in different P. trichocarpa genotypes    Table S5. List of genes in introgressed region from chromosome 6 and 15 based on local ancestry analysis in RASPberry.  Table S6. A  Introgressed genes from P. balsamifera in P. trichocarpa in a telomeric region of chromosome 15, corresponding Arabidopsis ortholog gene code, GO term or protein group enriched in the introgressed regions, Tajima's D values higher than 99% of the distribution, genes with significant positive values of alpha and nucleotide diversity values higher than 95% of the distribution in P. balsamifera Table S6B Genes from 280 kb to 880 kb from region B in chromosome 15 and region A in chromosome 6 associated with GO terms and protein groups enriched in the introgressed regions from P.balsamifera into P. trichocarpa  Table S7. List of genes in introgressed region B in chromosome 15 that showed significantly different levels of expression in admixed (bb, bt) individuals compared to pure P. trichocarpa individuals  Table S8. A Genes from the first introgressed region of chromosome 15 that showed associations with traits related to phenology, ecophysiology and biomass (McKown et at. 2014)    Table S1. List of P. trichocarpa and P. balsamifera accessions used in this study and biogeographical data (latitude, longitude, elevation). Data generated by this study is highlighted in orange (i.e.SNPs for local ancestry analysis, RASPberry; and gene sequence analysis. See M&M and Supplementary Figure 2). Data previously published is highlighted in blue (i.e. phenotypic data, McKown et at. 2013, DOI: 10.1111/nph.12601, S2 in nph12601-sup-0002-TablesS1-S8.xlsx) and that in preparation is highlighted in purple (RNA-seq, O. Corea, S. Biswas et al., preparation; PCA and preliminary RASPberry analysis, Geraldes et al in preparation)  *P. trichocarpa individuals were classified in one of three genotypic categories: homozygotes for P. balsamifera haplotypes (bb), heterozygotes (bt) and homozygotes for P. trichocarpa haplotypes (tt), based on phased genomic sequences of one introgressed region in chromosome 15 † We mined a population-wide RNA-seq dataset derived from 385 RNA samples isolated from developing xylem in 197 accessions (most in at least duplicate), and from 389 RNA samples isolated from expanding leaves of defined developmental stage in 191 accessions (most in at least duplicate) grown at Totem Field (O. Corea, S. Biswas et al., preparation). Levels of gene expression (measured by FPKM values) were compared among the three genotypic categories (bb, bt and tt). AP individuals are genotypes from Alberta Pacific breeding program, supplied by Dr. Barbara Thomas. They do not belong to the core AgCanBaP collection. Accession Species code Drainage/Location name Lat Long Elevation Included in RASPberry analysis Gene sequence analysis Genotypic Categories* RNA-seq_replicates† Phenotype data  AP-31-1004 P. balsamifera Muskeg Creek, AB 55.24 114.36 630.00 Yes (admixed) No NA No No AP-31-1006 P. balsamifera Muskeg Creek, AB 55.11 114.03 625.00 Yes (admixed) No NA No No AP-31-2298 P. balsamifera Fort Nelson River, BC 59.11 122.46 266.00 Yes (admixed) No NA No No AP-31-2446 P. balsamifera Muskeg Creek, AB 55.24 114.36 630.00 Yes (admixed) No NA No No AP-31-5230 P. balsamifera Muskeg Creek, AB 55.24 114.36 630.00 Yes (admixed) No NA No No AP-31-5451 P. balsamifera Poplar Creek Road, AB 56.56 111.32 316.00 Yes (admixed) No NA No No AP-31-5452 P. balsamifera Calling Lake, AB 55.09 113.15 653.00 Yes (admixed) No NA No No AP-31-5454 P. balsamifera Marten Hills, AB 55.26 114.31 841.00 Yes (admixed) No NA No No BOY-31-1 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No BOY-31-11 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No BOY-31-12 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No BOY-31-2 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No   BOY-31-3 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No BOY-31-4 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No BOY-31-6 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No BOY-31-8 P. balsamifera Boyle 54.55 -112.65 649.00 No Yes NA No No CAR-31-1 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-11 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-12 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-13 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-14 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-2 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-20 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-24 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-4 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-7 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No CAR-31-8 P. balsamifera Carnduff 49.18 -101.83 558.00 No Yes NA No No DEN-31-1 P. balsamifera Denali National Park 63.39 -148.51 594.00 No Yes NA No No DEN-31-10 P. balsamifera Denali National Park 63.39 -148.51 594.00 No Yes NA No No DEN-31-13 P. balsamifera Denali National Park 63.39 -148.51 594.00 Yes (admixed) Yes NA No No DEN-31-3 P. balsamifera Denali National Park 63.39 -148.51 594.00 No Yes NA No No DEN-31-4 P. balsamifera Denali National Park 63.39 -148.51 594.00 Yes (admixed) Yes NA No No DEN-31-5 P. balsamifera Denali National Park 63.39 -148.51 594.00 No Yes NA No No DEN-31-7 P. balsamifera Denali National Park 63.39 -148.51 594.00 No Yes NA No No DESD-31-22 P. balsamifera Dease 59.45 -129.02 674.00 Yes (admixed) No NA No No DUN-31-1 P. balsamifera Dunlop 54.51 -98.35 223.00 No Yes NA No No DUN-31-10 P. balsamifera Dunlop 54.51 -98.35 223.00 No Yes NA No No   DUN-31-11 P. balsamifera Dunlop 54.51 -98.35 223.00 No Yes NA No No DUN-31-13 P. balsamifera Dunlop 54.51 -98.35 223.00 Yes (pure) Yes NA No No DUN-31-14 P. balsamifera Dunlop 54.51 -98.35 223.00 Yes (pure) Yes NA No No DUN-31-2 P. balsamifera Dunlop 54.51 -98.35 223.00 No Yes NA No No DUN-31-4 P. balsamifera Dunlop 54.51 -98.35 223.00 Yes (pure) Yes NA No No DUN-31-6 P. balsamifera Dunlop 54.51 -98.35 223.00 No Yes NA No No DUN-31-8 P. balsamifera Dunlop 54.51 -98.35 223.00 No Yes NA No No EDM-31-1 P. balsamifera Edmonton 53.55 -113.32 719.00 No Yes NA No No EDM-31-10 P. balsamifera Edmonton 53.55 -113.32 719.00 No Yes NA No No EDM-31-11 P. balsamifera Edmonton 53.55 -113.32 719.00 No Yes NA No No EDM-31-3 P. balsamifera Edmonton 53.55 -113.32 719.00 No Yes NA No No EDM-31-5 P. balsamifera Edmonton 53.55 -113.32 719.00 No Yes NA No No EDM-31-6 P. balsamifera Edmonton 53.55 -113.32 719.00 No Yes NA No No EDM-31-9 P. balsamifera Edmonton 53.55 -113.32 719.00 No Yes NA No No FBK-31-10 P. balsamifera Fairbanks 64.90 -146.35 248.00 No Yes NA No No FBK-31-11 P. balsamifera Fairbanks 64.90 -146.35 248.00 Yes (pure) Yes NA No No FBK-31-3 P. balsamifera Fairbanks 64.90 -146.35 248.00 No Yes NA No No FBK-31-4 P. balsamifera Fairbanks 64.90 -146.35 248.00 No Yes NA No No FBK-31-5 P. balsamifera Fairbanks 64.90 -146.35 248.00 No Yes NA No No FBK-31-6 P. balsamifera Fairbanks 64.90 -146.35 248.00 Yes (pure) Yes NA No No FBK-31-9 P. balsamifera Fairbanks 64.90 -146.35 248.00 No Yes NA No No FRE-31-12 P. balsamifera Frederiction 46.40 -67.25 147.00 No Yes NA No No FRE-31-14 P. balsamifera Frederiction 46.40 -67.25 147.00 No Yes NA No No FRE-31-5 P. balsamifera Frederiction 46.40 -67.25 147.00 No Yes NA No No FRE-31-6 P. balsamifera Frederiction 46.40 -67.25 147.00 No Yes NA No No FRE-31-8 P. balsamifera Frederiction 46.40 -67.25 147.00 No Yes NA No No FRE-31-9 P. balsamifera Frederiction 46.40 -67.25 147.00 No Yes NA No No FTM-31-1 P. balsamifera Fort McMurray 56.56 -111.36 338.00 No Yes NA No No   FTM-31-13 P. balsamifera Fort McMurray 56.56 -111.36 338.00 No Yes NA No No FTM-31-2 P. balsamifera Fort McMurray 56.56 -111.36 338.00 No Yes NA No No FTM-31-3 P. balsamifera Fort McMurray 56.56 -111.36 338.00 No Yes NA No No FTM-31-4 P. balsamifera Fort McMurray 56.56 -111.36 338.00 No Yes NA No No FTM-31-5 P. balsamifera Fort McMurray 56.56 -111.36 338.00 Yes (admixed) Yes NA No No FTM-31-6 P. balsamifera Fort McMurray 56.56 -111.36 338.00 Yes (admixed) Yes NA No No FTM-31-8 P. balsamifera Fort McMurray 56.56 -111.36 338.00 Yes (admixed) Yes NA No No FTM-31-9 P. balsamifera Fort McMurray 56.56 -111.36 338.00 No Yes NA No No GIL-31-1 P. balsamifera Gillam 56.35 -94.63 126.00 Yes (pure) No NA No No GIL-31-10 P. balsamifera Gillam 56.25 -94.36 126.00 Yes (pure) No NA No No GIL-31-14 P. balsamifera Gillam 56.25 -94.36 126.00 No Yes NA No No GIL-31-3 P. balsamifera Gillam 56.25 -94.36 126.00 No Yes NA No No GIL-31-4 P. balsamifera Gillam 56.25 -94.36 126.00 No Yes NA No No GIL-31-7 P. balsamifera Gillam 56.25 -94.36 126.00 No Yes NA No No GIL-31-8 P. balsamifera Gillam 56.25 -94.36 126.00 No Yes NA No No GPR-31-1 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-10 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) No NA No No GPR-31-11 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-12 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-13 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-14 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) No NA No No GPR-31-2 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-3 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-4 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes No NA No No   (admixed) GPR-31-5 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-6 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) No NA No No GPR-31-7 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) Yes NA No No GPR-31-8 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) No NA No No GPR-31-9 P. balsamifera Grande Prairie 54.75 -118.63 769.00 Yes (admixed) No NA No No GRA-31-10 P. balsamifera Grand Rapids 53.20 -99.35 254.00 No Yes NA No No GRA-31-3 P. balsamifera Grand Rapids 53.20 -99.35 254.00 No Yes NA No No GRA-31-4 P. balsamifera Grand Rapids 53.20 -99.35 254.00 No Yes NA No No GRA-31-5 P. balsamifera Grand Rapids 53.20 -99.35 254.00 No Yes NA No No GRA-31-6 P. balsamifera Grand Rapids 53.20 -99.35 254.00 No Yes NA No No GRA-31-7 P. balsamifera Grand Rapids 53.20 -99.35 254.00 No Yes NA No No GRA-31-8 P. balsamifera Grand Rapids 53.20 -99.35 254.00 No Yes NA No No GYP-31-1 P. balsamifera Gypsumville 51.77 -98.62 253.00 No Yes NA No No GYP-31-10 P. balsamifera Gypsumville 51.77 -98.62 253.00 Yes (pure) Yes NA No No GYP-31-12 P. balsamifera Gypsumville 51.77 -98.62 253.00 No Yes NA No No GYP-31-13 P. balsamifera Gypsumville 51.77 -98.62 253.00 Yes (pure) No NA No No GYP-31-2 P. balsamifera Gypsumville 51.77 -98.62 253.00 No Yes NA No No GYP-31-3 P. balsamifera Gypsumville 51.77 -98.62 253.00 No Yes NA No No GYP-31-4 P. balsamifera Gypsumville 51.77 -98.62 253.00 No Yes NA No No GYP-31-7 P. balsamifera Gypsumville 51.77 -98.62 253.00 No Yes NA No No GYP-31-9 P. balsamifera Gypsumville 51.77 -98.62 253.00 Yes (pure) No NA No No HAY-31-1 P. balsamifera Hay River 60.80 -115.78 168.00 No Yes NA No No HAY-31-11 P. balsamifera Hay River 60.80 -115.78 168.00 No Yes NA No No HAY-31-12 P. balsamifera Hay River 60.80 -115.78 168.00 No Yes NA No No   HAY-31-3 P. balsamifera Hay River 60.80 -115.78 168.00 No Yes NA No No HAY-31-4 P. balsamifera Hay River 60.80 -115.78 168.00 No Yes NA No No HAY-31-5 P. balsamifera Hay River 60.80 -115.78 168.00 No Yes NA No No INU-31-9 P. balsamifera Inuvik 68.38 -133.77 7.00 Yes (pure) No NA No No KUU-31-09 P. balsamifera Kuujjuaq 58.02 -68.65 17.00 No Yes NA No No KUU-31-1 P. balsamifera Kuujjuaq 58.02 -68.65 17.00 No Yes NA No No KUU-31-10 P. balsamifera Kuujjuaq 58.02 -68.65 17.00 No Yes NA No No KUU-31-13 P. balsamifera Kuujjuaq 58.02 -68.65 17.00 No Yes NA No No KUU-31-2 P. balsamifera Kuujjuaq 58.02 -68.65 17.00 No Yes NA No No KUU-31-3 P. balsamifera Kuujjuaq 58.02 -68.65 17.00 No Yes NA No No KUU-31-5 P. balsamifera Kuujjuaq 58.02 -68.65 17.00 No Yes NA No No LAB-31-1 P. balsamifera Labrador City 52.93 -67.25 554.00 No Yes NA No No LAB-31-12 P. balsamifera Labrador City 52.93 -67.25 554.00 No Yes NA No No LAB-31-4 P. balsamifera Labrador City 52.93 -67.25 554.00 No Yes NA No No LAB-31-5 P. balsamifera Labrador City 52.93 -67.25 554.00 No Yes NA No No LAB-31-6 P. balsamifera Labrador City 52.93 -67.25 554.00 No Yes NA No No LAB-31-7 P. balsamifera Labrador City 52.93 -67.25 554.00 No Yes NA No No LAB-31-8 P. balsamifera Labrador City 52.93 -67.25 554.00 No Yes NA No No LAR-31-11 P. balsamifera La Ronge 54.45 -105.33 471.00 No Yes NA No No LAR-31-12 P. balsamifera La Ronge 54.45 -105.33 471.00 Yes (pure) No NA No No LAR-31-15 P. balsamifera La Ronge 54.45 -105.33 471.00 No Yes NA No No LAR-31-2 P. balsamifera La Ronge 54.45 -105.33 471.00 No Yes NA No No LAR-31-3 P. balsamifera La Ronge 54.45 -105.33 471.00 No Yes NA No No LAR-31-5 P. balsamifera La Ronge 54.45 -105.33 471.00 No Yes NA No No LAR-31-6 P. balsamifera La Ronge 54.45 -105.33 471.00 No Yes NA No No LAR-31-9 P. balsamifera La Ronge 54.45 -105.33 471.00 No Yes NA No No LOV-31-1 P. balsamifera Love 53.63 -105.50 419.00 No Yes NA No No LOV-31- P. balsamifera Love 53.63 -105.50 419.00 No Yes NA No No   11 LOV-31-2 P. balsamifera Love 53.63 -105.50 419.00 No Yes NA No No LOV-31-3 P. balsamifera Love 53.63 -105.50 419.00 No Yes NA No No LOV-31-4 P. balsamifera Love 53.63 -105.50 419.00 No Yes NA No No LOV-31-6 P. balsamifera Love 53.63 -105.50 419.00 No Yes NA No No LOV-31-7 P. balsamifera Love 53.63 -105.50 419.00 No Yes NA No No MAN-31-2 P. balsamifera Manicougan 49.30 -68.32 180.00 No Yes NA No No MAN-31-4 P. balsamifera Manicougan 49.30 -68.32 180.00 No Yes NA No No MAN-31-5 P. balsamifera Manicougan 49.30 -68.32 180.00 No Yes NA No No MAN-31-7 P. balsamifera Manicougan 49.30 -68.32 180.00 No Yes NA No No MAN-31-9 P. balsamifera Manicougan 49.30 -68.32 180.00 No Yes NA No No MAT-31-11 P. balsamifera Matapedia 48.22 -67.18 98.00 No Yes NA No No MAT-31-12 P. balsamifera Matapedia 48.22 -67.18 98.00 No Yes NA No No MAT-31-14 P. balsamifera Matapedia 48.22 -67.18 98.00 No Yes NA No No MAT-31-2 P. balsamifera Matapedia 48.22 -67.18 98.00 No Yes NA No No MAT-31-3 P. balsamifera Matapedia 48.22 -67.18 98.00 No Yes NA No No MAT-31-4 P. balsamifera Matapedia 48.22 -67.18 98.00 No Yes NA No No MAT-31-7 P. balsamifera Matapedia 48.22 -67.18 98.00 No Yes NA No No MEL-31-11 P. balsamifera Melville 51.35 -102.62 541.00 No Yes NA No No MEL-31-12 P. balsamifera Melville 51.35 -102.62 541.00 No Yes NA No No MEL-31-2 P. balsamifera Melville 51.35 -102.62 541.00 Yes (pure) No NA No No MEL-31-4 P. balsamifera Melville 51.35 -102.62 541.00 No Yes NA No No MEL-31-5 P. balsamifera Melville 51.35 -102.62 541.00 No Yes NA No No MEL-31-6 P. balsamifera Melville 51.35 -102.62 541.00 No Yes NA No No MEL-31-7 P. balsamifera Melville 51.35 -102.62 541.00 No Yes NA No No MGR-31- P. balsamifera Mount Groulx 51.33 68.09 na No Yes NA No No   11 MGR-31-3 P. balsamifera Mount Groulx 51.33 68.09 na No Yes NA No No MGR-31-4 P. balsamifera Mount Groulx 51.33 68.09 na No Yes NA No No MGR-31-5 P. balsamifera Mount Groulx 51.33 68.09 na No Yes NA No No MGR-31-8 P. balsamifera Mount Groulx 51.33 68.09 na No Yes NA No No MGR-31-9 P. balsamifera Mount Groulx 51.33 68.09 na No Yes NA No No MIN-31-1 P. balsamifera Minnedosa 50.32 -99.85 592.00 Yes (pure) Yes NA No No MIN-31-10 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MIN-31-11 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MIN-31-13 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MIN-31-14 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MIN-31-2 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MIN-31-3 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MIN-31-4 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MIN-31-9 P. balsamifera Minnedosa 50.32 -99.85 592.00 No Yes NA No No MTN-31-10 P. balsamifera Matane 48.57 -67.35 119.00 No Yes NA No No MTN-31-11 P. balsamifera Matane 48.57 -67.35 119.00 No Yes NA No No MTN-31-13 P. balsamifera Matane 48.57 -67.35 119.00 No Yes NA No No MTN-31-2 P. balsamifera Matane 48.57 -67.35 119.00 No Yes NA No No MTN-31-3 P. balsamifera Matane 48.57 -67.35 119.00 No Yes NA No No MTN-31-9 P. balsamifera Matane 48.57 -67.35 119.00 No Yes NA No No NWL-31-1 P. balsamifera Norman Wells 65.16 -126.44 84.00 Yes (pure) No NA No No NWL-31-10 P. balsamifera Norman Wells 65.16 -126.44 84.00 Yes (pure) Yes NA No No   NWL-31-11 P. balsamifera Norman Wells 65.16 -126.44 84.00 Yes (pure) No NA No No NWL-31-112 P. balsamifera Norman Wells 65.16 -126.44 84.00 Yes (pure) No NA No No NWL-31-12 P. balsamifera Norman Wells 65.16 -126.44 84.00 Yes (pure) Yes NA No No NWL-31-16 P. balsamifera Norman Wells 65.16 -126.44 84.00 No Yes NA No No NWL-31-2 P. balsamifera Norman Wells 65.16 -126.44 84.00 No Yes NA No No NWL-31-3 P. balsamifera Norman Wells 65.16 -126.44 84.00 No Yes NA No No NWL-31-5 P. balsamifera Norman Wells 65.16 -126.44 84.00 No Yes NA No No NWL-31-7 P. balsamifera Norman Wells 65.16 -126.44 84.00 Yes (pure) No NA No No NWL-31-8 P. balsamifera Norman Wells 65.16 -126.44 84.00 No Yes NA No No NWL-31-9 P. balsamifera Norman Wells 65.23 -126.67 84.00 Yes (pure) No NA No No POR-31-1 P. balsamifera Portage 49.57 -98.18 283.00 No Yes NA No No POR-31-11 P. balsamifera Portage 49.57 -98.18 283.00 No Yes NA No No POR-31-12 P. balsamifera Portage 49.57 -98.18 283.00 No Yes NA No No POR-31-14 P. balsamifera Portage 49.57 -98.18 283.00 No Yes NA No No POR-31-4 P. balsamifera Portage 49.57 -98.18 283.00 No Yes NA No No POR-31-5 P. balsamifera Portage 49.57 -98.18 283.00 No Yes NA No No POR-31-6 P. balsamifera Portage 49.57 -98.18 283.00 Yes (pure) Yes NA No No POR-31-7 P. balsamifera Portage 49.57 -98.18 283.00 No Yes NA No No RNA-31-1 P. balsamifera Rouyn-Noranda 48.60 -78.67 310.00 No Yes NA No No RNA-31-11 P. balsamifera Rouyn-Noranda 48.60 -78.67 310.00 No Yes NA No No RNA-31-13 P. balsamifera Rouyn-Noranda 48.60 -78.67 310.00 No Yes NA No No RNA-31-14 P. balsamifera Rouyn-Noranda 48.60 -78.67 310.00 No Yes NA No No RNA-31-2 P. balsamifera Rouyn-Noranda 48.60 -78.67 310.00 No Yes NA No No RNA-31-3 P. balsamifera Rouyn-Noranda 48.60 -78.67 310.00 No Yes NA No No RNA-31-6 P. balsamifera Rouyn-Noranda 48.60 -78.67 310.00 No Yes NA No No ROS-31-1 P. balsamifera Roseville 47.33 -64.37 25.00 No Yes NA No No   ROS-31-14 P. balsamifera Roseville 47.33 -64.37 25.00 No Yes NA No No ROS-31-4 P. balsamifera Roseville 47.33 -64.37 25.00 No Yes NA No No ROS-31-6 P. balsamifera Roseville 47.33 -64.37 25.00 No Yes NA No No ROS-31-9 P. balsamifera Roseville 47.33 -64.37 25.00 No Yes NA No No SOU-31-1 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-12 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-14 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-15 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-2 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-3 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-4 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-5 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-7 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SOU-31-9 P. balsamifera Sioux Lookout 50.08 -91.90 384.00 No Yes NA No No SRD-31-11 P. balsamifera South Reindeer 56.27 -104.23 419.00 No Yes NA No No SRD-31-12 P. balsamifera South Reindeer 56.27 -104.23 419.00 No Yes NA No No SRD-31-2 P. balsamifera South Reindeer 56.27 -104.23 419.00 No Yes NA No No SRD-31-4 P. balsamifera South Reindeer 56.27 -104.23 419.00 No Yes NA No No SRD-31-5 P. balsamifera South Reindeer 56.27 -104.23 419.00 No Yes NA No No SRD-31-7 P. balsamifera South Reindeer 56.27 -104.23 419.00 No Yes NA No No SRD-31-8 P. balsamifera South Reindeer 56.27 -104.23 419.00 No Yes NA No No SRD-31-9 P. balsamifera South Reindeer 56.27 -104.23 419.00 Yes (admixed) Yes NA No No STL-31-1 P. balsamifera Stettler 52.35 -112.73 795.00 No Yes NA No No STL-31-10 P. balsamifera Stettler 52.35 -112.73 795.00 No Yes NA No No STL-31-13 P. balsamifera Stettler 52.35 -112.73 795.00 No Yes NA No No STL-31-14 P. balsamifera Stettler 52.35 -112.73 795.00 No Yes NA No No STL-31-8 P. balsamifera Stettler 52.35 -112.73 795.00 No Yes NA No No STO-31-1 P. balsamifera Stony Rapids 59.23 -105.72 306.00 No Yes NA No No   STO-31-12 P. balsamifera Stony Rapids 59.23 -105.72 306.00 No Yes NA No No STO-31-13 P. balsamifera Stony Rapids 59.23 -105.72 306.00 No Yes NA No No STO-31-2 P. balsamifera Stony Rapids 59.23 -105.72 306.00 No Yes NA No No STO-31-4 P. balsamifera Stony Rapids 59.23 -105.72 306.00 No Yes NA No No STO-31-7 P. balsamifera Stony Rapids 59.23 -105.72 306.00 No Yes NA No No STO-31-8 P. balsamifera Stony Rapids 59.23 -105.72 306.00 No Yes NA No No TNZA-4-1 P. balsamifera Upper Stikine 58.30 -130.47 567.00 Yes (admixed) Yes NA No No WAD-31-1 P. balsamifera Wadena 52.37 -104.27 543.00 No Yes NA No No WAD-31-1 P. balsamifera Wadena 52.37 -104.27 543.00 Yes (pure) No NA No No WAD-31-12 P. balsamifera Wadena 52.37 -104.27 543.00 No Yes NA No No WAD-31-14 P. balsamifera Wadena 52.37 -104.27 543.00 No Yes NA No No WAD-31-3 P. balsamifera Wadena 52.37 -104.27 543.00 No Yes NA No No WAD-31-5 P. balsamifera Wadena 52.37 -104.27 543.00 No Yes NA No No WAD-31-8 P. balsamifera Wadena 52.37 -104.27 543.00 No Yes NA No No WHR-31-1 P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No WHR-31-11 P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No WHR-31-11 P. balsamifera Whitehorse 60.70 -135.33 770.00 Yes (admixed) No NA No No WHR-31-12 P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No WHR-31-15 P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No WHR-31-2 P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No WHR-31- P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No   3 WHR-31-3 P. balsamifera Whitehorse 60.70 -135.33 770.00 Yes (pure) No NA No No WHR-31-4 P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No WHR-31-4 P. balsamifera White Horse 60.70 -135.33 770.00 Yes (pure) No NA No No WHR-31-9 P. balsamifera Whitehorse 60.70 -135.33 770.00 No Yes NA No No WOL-31-1 P. balsamifera Wollaston Lake 57.58 -103.93 423.00 No Yes NA No No WOL-31-14 P. balsamifera Wollaston Lake 57.58 -103.93 423.00 No Yes NA No No WOL-31-15 P. balsamifera Wollaston Lake 57.58 -103.93 423.00 No Yes NA No No WOL-31-2 P. balsamifera Wollaston Lake 57.58 -103.93 423.00 No Yes NA No No WOL-31-3 P. balsamifera Wollaston Lake 57.58 -103.93 423.00 No Yes NA No No WOL-31-4 P. balsamifera Wollaston Lake 57.58 -103.93 423.00 No Yes NA No No WOL-31-6 P. balsamifera Wollaston Lake 57.58 -103.93 423.00 Yes (admixed) Yes NA No No ALAA-20-1 P. trichocarpa Klinaklini 50.98 -126.12 0.00 Yes (pure) Yes NA No No ALAA-20-3 P. trichocarpa Klinaklini 50.98 -126.12 0.00 No Yes NA No No ALAA-20-4 P. trichocarpa Klinaklini 50.98 -126.12 0.00 No Yes NA No No ALAA-20-5 P. trichocarpa Klinaklini 50.98 -126.12 0.00 No Yes NA No No ALSC-1-4 P. trichocarpa Alsek 59.62 -137.92 107.00 Yes (admixed) Yes bt No Yes ALSC-1-5 P. trichocarpa Alsek 59.62 -137.92 107.00 Yes (admixed) Yes bt No Yes AMER-13-1 P. trichocarpa Stuart 54.63 -124.97 701.00 Yes (pure) Yes tt 14 No AMER-13-3 P. trichocarpa Stuart 54.63 -124.97 701.00 No Yes tt No No BELA-18-1 P. trichocarpa Bella Coola river 52.42 -126.17 152.00 No Yes NA No No   BELA-18-2 P. trichocarpa Bella Coola river 52.42 -126.17 152.00 No Yes NA No No BELA-18-3 P. trichocarpa Bella Coola river 52.42 -126.17 152.00 No Yes NA No No BELA-18-5 P. trichocarpa Bella Coola river 52.42 -126.17 152.00 No Yes NA No No BELC-18-1 P. trichocarpa Bella Coola river 52.38 -126.60 135.00 No Yes NA No No BELC-18-2 P. trichocarpa Bella Coola river 52.38 -126.60 135.00 No Yes NA No No BELC-18-3 P. trichocarpa Bella Coola river 52.38 -126.60 135.00 No Yes NA No No BELC-18-4 P. trichocarpa Bella Coola river 52.38 -126.60 135.00 No Yes NA No No BELC-18-5 P. trichocarpa Bella Coola river 52.38 -126.60 135.00 No Yes NA No No BULA-11-4 P. trichocarpa Bulkley 55.25 -127.50 311.00 Yes (admixed) Yes bt No Yes BULB-11-1 P. trichocarpa Bulkley 55.12 -127.35 427.00 No Yes tt No Yes BULF-11-2 P. trichocarpa Bulkley 54.55 -126.83 561.00 No Yes tt No Yes BULF-11-3 P. trichocarpa Bulkley 54.55 -126.83 561.00 No Yes tt No Yes BULF-11-4 P. trichocarpa Bulkley 54.55 -126.83 561.00 No Yes tt No Yes BULF-11-5 P. trichocarpa Bulkley 54.55 -126.83 561.00 No Yes tt No Yes BULG-11-2 P. trichocarpa Bulkley 54.45 -126.80 579.00 No Yes bt No Yes BULG-11-4 P. trichocarpa Bulkley 54.45 -126.80 579.00 No Yes tt No Yes BULG-11-5 P. trichocarpa Bulkley 54.45 -126.80 579.00 No Yes tt No Yes CARS-29-2 P. trichocarpa Columbia 45.75 -122.83 650.00 No Yes NA No No CARS-29-3 P. trichocarpa Columbia 45.75 -122.83 650.00 No Yes NA No No CARS-29-4 P. trichocarpa Columbia 45.75 -122.83 650.00 No Yes NA No No CARS-29-5 P. trichocarpa Columbia 45.75 -122.83 650.00 No Yes NA No No   CDRE-10-1 P. trichocarpa Skeena 55.02 -128.33 152.00 No Yes tt No Yes CDRE-10-3 P. trichocarpa Skeena 55.02 -128.33 152.00 No Yes tt No Yes CEDA-10-2 P. trichocarpa Skeena 54.95 -128.92 274.00 No Yes tt No Yes CEDA-10-4 P. trichocarpa Skeena 54.95 -128.92 274.00 No Yes tt No Yes CHIL-14-2 P. trichocarpa Nechako 54.88 -122.98 183.00 No Yes tt No Yes CHKC-19-1 P. trichocarpa Chuckwall 51.73 -127.32 67.00 No Yes NA No No CHKC-19-2 P. trichocarpa Chuckwall 51.73 -127.32 67.00 No Yes NA No No CHKC-19-3 P. trichocarpa Chuckwall 51.73 -127.32 67.00 No Yes NA No No CHKC-19-4 P. trichocarpa Chuckwall 51.77 -127.20 79.00 Yes (pure) Yes NA No No CHKD-19-1 P. trichocarpa Chuckwall 51.77 -127.20 79.00 No Yes NA No No CHKD-19-2 P. trichocarpa Chuckwall 51.77 -127.20 79.00 No Yes NA No No CHKD-19-3 P. trichocarpa Chuckwall 51.77 -127.20 79.00 No Yes NA No No CHKD-19-4 P. trichocarpa Chuckwall 51.77 -127.20 79.00 No Yes NA No No CHKD-19-5 P. trichocarpa Chuckwall 51.77 -127.20 79.00 No Yes NA No No CHNH-27-4 P. trichocarpa Fraser 49.08 -121.72 280.00 No Yes NA No No CHWJ-27-2 P. trichocarpa Fraser 49.08 -121.72 280.00 Yes (pure) No NA No No CNYH-28-1 P. trichocarpa Vancouver Island 49.67 -125.07 76.00 No Yes NA No No CNYH-28-2 P. trichocarpa Vancouver Island 49.67 -125.07 76.00 Yes (pure) No NA No No CSYJ-28-1 P. trichocarpa Vancouver Island 49.07 -123.87 20.00 No Yes NA No No CSYJ-28-2 P. trichocarpa Vancouver Island 49.07 -123.87 20.00 No Yes NA No No   CSYJ-28-3 P. trichocarpa Vancouver Island 49.07 -123.87 20.00 No Yes NA No No CSYJ-28-4 P. trichocarpa Vancouver Island 49.07 -123.87 20.00 No Yes NA No No DENB-17-2 P. trichocarpa Dean 52.83 -126.70 152.00 Yes (pure) No NA No No ELAD-25-1 P. trichocarpa Squamish 50.25 -123.58 305.00 No Yes NA No No ELAD-25-2 P. trichocarpa Squamish 50.25 -123.58 305.00 No Yes NA No No ELAD-25-3 P. trichocarpa Squamish 50.25 -123.58 305.00 No Yes NA No No ELAD-25-4 P. trichocarpa Squamish 50.25 -123.58 305.00 No Yes NA No No ELAD-25-5 P. trichocarpa Squamish 50.25 -123.58 305.00 No Yes NA No No FKRB-6-1 P. trichocarpa Iskut 56.73 -130.63 280.00 No Yes tt No Yes GLCB-26-3 P. trichocarpa Lillooet 50.10 -123.00 579.00 Yes (pure) No NA No No HALS-30-1 P. trichocarpa Willamette 44.42 -123.33 300.00 No Yes NA No No HALS-30-2 P. trichocarpa Willamette 44.42 -123.33 300.00 No Yes NA No No HALS-30-4 P. trichocarpa Willamette 44.42 -123.33 300.00 No Yes NA No No HALS-30-6 P. trichocarpa Willamette 44.42 -123.33 300.00 No Yes NA No No HAZH-10-1 P. trichocarpa Skeena 55.22 -127.67 238.00 No Yes tt No Yes HAZH-10-2 P. trichocarpa Skeena 55.22 -127.67 238.00 No Yes tt 2 Yes HAZH-10-3 P. trichocarpa Skeena 55.22 -127.67 238.00 No Yes bt No Yes HAZH-10-5 P. trichocarpa Skeena 55.22 -127.67 238.00 No Yes bt No Yes HIRD-12-2 P. trichocarpa Kitimat 54.07 -128.45 335.00 No No tt 2 Yes HIXN-16-1 P. trichocarpa Quesnel 53.40 -122.63 518.00 Yes (admixed) Yes tt 2 Yes   HIXN-16-5 P. trichocarpa Quesnel 53.40 -122.63 518.00 Yes (admixed) Yes tt No Yes HOMB-21-1 P. trichocarpa Homathko 51.23 -124.95 88.00 Yes (pure) Yes NA No No HOMB-21-5 P. trichocarpa Homathko 50.95 -124.90 37.00 No Yes NA No No HOMD-21-5 P. trichocarpa Homathko 51.28 -124.83 152.00 No Yes NA No No HOPF-27-2 P. trichocarpa Fraser 49.43 -121.43 61.00 No Yes NA No No HOPF-27-4 P. trichocarpa Fraser 49.43 -121.43 61.00 No Yes NA No No HOPG-27-1 P. trichocarpa Fraser 49.40 -121.55 500.00 No Yes NA No No HRSP-27-3 P. trichocarpa Fraser 49.23 -121.85 30.00 No Yes NA No No IRVC-7-1 P. trichocarpa Bell-Irving 56.73 -129.73 579.00 No Yes tt No Yes IRVC-7-4 P. trichocarpa Bell-Irving 56.73 -129.73 579.00 No Yes tt No Yes IRVC-7-5 P. trichocarpa Bell-Irving 56.73 -129.73 579.00 No Yes bt No Yes IRVC-7-6 P. trichocarpa Bell-Irving 56.73 -129.73 579.00 No Yes tt No Yes IRVD-7-4 P. trichocarpa Bell-Irving 56.85 -129.62 677.00 Yes (admixed) Yes bt No Yes ISKA-6-1 P. trichocarpa Iskut 56.70 -131.15 73.00 No Yes tt No Yes ISKA-6-2 P. trichocarpa Iskut 56.70 -131.15 73.00 No Yes tt No Yes ISKA-6-4 P. trichocarpa Iskut 56.70 -131.15 73.00 No Yes tt No Yes ISKA-6-5 P. trichocarpa Iskut 56.70 -131.15 73.00 No Yes bt No No ISKC-6-1 P. trichocarpa Iskut 56.93 -130.33 317.00 No Yes bt No No ISKC-6-2 P. trichocarpa Iskut 56.93 -130.33 317.00 No Yes NA No No ISKC-6-3 P. trichocarpa Iskut 56.93 -130.33 317.00 No Yes tt No Yes ISKC-6-5 P. trichocarpa Iskut 56.93 -130.33 317.00 No Yes tt No Yes JASP-30-1 P. trichocarpa Willamette 44.00 -122.92 150.00 No Yes NA No No JASP-30-3 P. trichocarpa Willamette 44.00 -122.92 150.00 No Yes NA No No JASP-30-4 P. trichocarpa Willamette 44.00 -122.92 150.00 No Yes NA No No JASP-30-5 P. trichocarpa Willamette 44.00 -122.92 150.00 No Yes NA No No JEFF-30-1 P. trichocarpa Willamette 44.73 -123.08 100.00 No Yes NA No No   JEFF-30-2 P. trichocarpa Willamette 44.73 -123.08 100.00 No Yes NA No No JEFF-30-3 P. trichocarpa Willamette 44.73 -123.08 100.00 No Yes NA No No JEFF-30-4 P. trichocarpa Willamette 44.73 -123.08 100.00 No Yes NA No No KIMB-16-1 P. trichocarpa Quesnel 52.93 -121.17 823.00 Yes (admixed) Yes tt No Yes KIMB-16-2 P. trichocarpa Quesnel 52.93 -121.17 823.00 Yes (pure) Yes tt 2 Yes KIMB-16-3 P. trichocarpa Quesnel 52.93 -121.17 823.00 Yes (admixed) Yes bt 2 Yes KIMB-16-4 P. trichocarpa Quesnel 52.93 -121.17 823.00 No Yes bt No Yes KIMB-16-5 P. trichocarpa Quesnel 52.93 -121.17 823.00 Yes (admixed) Yes tt No Yes KIMB-16-6 P. trichocarpa Quesnel 52.93 -121.17 823.00 Yes (admixed) Yes bb No Yes KLNE-20-1 P. trichocarpa Klinaklini 51.73 -125.57 427.00 No Yes NA No No KLNE-20-2 P. trichocarpa Klinaklini 51.73 -125.57 427.00 No Yes NA No No KSPA-9-3 P. trichocarpa Kispiox 55.77 -128.53 518.00 No Yes tt No Yes KTMA-12-1 P. trichocarpa Kitimat 54.25 -128.52 122.00 Yes (pure) No tt 2 Yes KTMA-12-2 P. trichocarpa Kitimat 54.25 -128.52 122.00 Yes (pure) No NA No No KTMA-12-3 P. trichocarpa Kitimat 54.25 -128.52 122.00 No No tt No Yes KTMA-12-4 P. trichocarpa Kitimat 54.25 -128.52 122.00 No No tt 2 Yes KTMA-12-5 P. trichocarpa Kitimat 54.25 -128.52 122.00 No Yes tt No Yes KTMB-12-1 P. trichocarpa Kitimat 54.15 -128.58 61.00 No Yes tt No No KTMB-12-3 P. trichocarpa Kitimat 54.15 -128.58 61.00 No Yes tt No No KTMB-12-5 P. trichocarpa Kitimat 54.15 -128.58 61.00 No Yes tt No No KTMC-12- P. trichocarpa Kitimat 54.05 -128.68 18.00 No No tt No Yes   1 KTMC-12-2 P. trichocarpa Kitimat 54.05 -128.68 18.00 No No tt No Yes KTMC-12-3 P. trichocarpa Kitimat 54.05 -128.68 18.00 No No tt 2 Yes KTMC-12-5 P. trichocarpa Kitimat 54.05 -128.68 18.00 No No tt 2 Yes KTSG-10-5 P. trichocarpa Skeena 55.10 -127.92 213.00 No Yes tt No Yes KTWF-10-3 P. trichocarpa Skeena 55.08 -128.18 177.00 No Yes tt No Yes LAFY-30-1 P. trichocarpa Willamette 45.20 -123.08 100.00 No Yes NA No No LAFY-30-2 P. trichocarpa Willamette 45.20 -123.08 100.00 No Yes NA No No LAFY-30-3 P. trichocarpa Willamette 45.20 -123.08 100.00 No Yes NA No No LAFY-30-5 P. trichocarpa Willamette 45.20 -123.08 100.00 No Yes NA No No LILA-26-3 P. trichocarpa Lillooet 50.62 -123.38 411.00 No Yes NA No No LILB-26-2 P. trichocarpa Lillooet 50.55 -123.20 274.00 No Yes NA No No LNZK-28-2 P. trichocarpa Vancouver Island 49.23 -124.07 60.00 No Yes NA No No LNZK-28-3 P. trichocarpa Vancouver Island 49.23 -124.07 60.00 No Yes NA No No LNZK-28-4 P. trichocarpa Vancouver Island 49.23 -124.07 60.00 No Yes NA No No LNZK-28-5 P. trichocarpa Vancouver Island 49.23 -124.07 60.00 No Yes NA No No LONG-29-1 P. trichocarpa Columbia 46.08 -123.92 100.00 No Yes NA No No LONG-29-2 P. trichocarpa Columbia 46.08 -123.92 100.00 No Yes NA No No LONG-29-3 P. trichocarpa Columbia 46.08 -123.92 100.00 No Yes NA No No LONG-29-4 P. trichocarpa Columbia 46.08 -123.92 100.00 No Yes NA No No LONG-29-5 P. trichocarpa Columbia 46.08 -123.92 100.00 No Yes NA No No MCFA-20- P. trichocarpa Klinaklini 51.32 -126.23 275.00 No Yes NA No No   1 MCFA-20-2 P. trichocarpa Klinaklini 51.32 -126.23 275.00 No Yes NA No No MCFA-20-3 P. trichocarpa Klinaklini 51.32 -126.23 275.00 No Yes NA No No MCFA-20-4 P. trichocarpa Klinaklini 51.32 -126.23 275.00 No Yes NA No No MCFA-20-5 P. trichocarpa Klinaklini 51.32 -126.23 275.00 No Yes NA No No MCFA-20-6 P. trichocarpa Klinaklini 51.32 -126.23 275.00 No Yes NA No No MCGR-15-4 P. trichocarpa McGregor 54.18 -122.00 579.00 No Yes tt No Yes MCGR-15-6 P. trichocarpa McGregor 54.18 -122.00 579.00 No Yes bt No Yes MCGR-15-7 P. trichocarpa McGregor 54.18 -122.00 579.00 No Yes tt No Yes MCGR-15-8 P. trichocarpa McGregor 54.18 -122.00 579.00 Yes (admixed) Yes bb No Yes MCHA-19-1 P. trichocarpa Chuckwall 51.63 -126.68 70.00 No Yes NA No No MCHA-19-2 P. trichocarpa Chuckwall 51.63 -126.68 70.00 No Yes NA No No MCHA-19-3 P. trichocarpa Chuckwall 51.63 -126.68 70.00 No Yes NA No No MCHA-19-4 P. trichocarpa Chuckwall 51.63 -126.68 70.00 No Yes NA No No MCHA-19-5 P. trichocarpa Chuckwall 51.63 -126.68 70.00 No Yes NA No No MCHB-19-1 P. trichocarpa Chuckwall 51.62 -126.58 122.00 No Yes NA No No MCHB-19-2 P. trichocarpa Chuckwall 51.62 -126.58 122.00 No Yes NA No No MCHB-19-3 P. trichocarpa Chuckwall 51.62 -126.58 122.00 No Yes NA No No MCHB-19-4 P. trichocarpa Chuckwall 51.62 -126.58 122.00 Yes (pure) No NA No No   MCHB-19-4 P. trichocarpa Chuckwall 51.62 -126.58 122.00 No Yes NA No No MCHB-19-5 P. trichocarpa Chuckwall 51.62 -126.58 122.00 No Yes NA No No MCMN-27-3 P. trichocarpa Fraser 49.18 -122.58 15.00 Yes (pure) No NA No No MEMA-28-1 P. trichocarpa Vancouver Island 50.22 -125.80 30.00 No Yes NA No No MEMA-28-3 P. trichocarpa Vancouver Island 50.22 -125.80 30.00 No Yes NA No No MEMA-28-4 P. trichocarpa Vancouver Island 50.22 -125.80 30.00 No Yes NA No No MEMA-28-5 P. trichocarpa Vancouver Island 50.22 -125.80 30.00 No Yes NA No No MTSM-27-2 P. trichocarpa Fraser 49.12 -122.33 8.00 No Yes NA No No MTSM-27-5 P. trichocarpa Fraser 49.12 -122.33 8.00 No Yes NA No No NASC-8-2 P. trichocarpa Nass 55.05 -129.50 24.00 No Yes tt No Yes NASC-8-5 P. trichocarpa Nass 55.05 -129.50 24.00 No Yes bt No Yes NASD-8-2 P. trichocarpa Nass 55.05 -129.50 24.00 No Yes NA No No NASD-8-4 P. trichocarpa Nass 55.22 -129.13 58.00 No Yes tt No Yes NASD-8-5 P. trichocarpa Nass 55.22 -129.13 58.00 No Yes tt No Yes NASF-8-2 P. trichocarpa Nass 55.57 -128.78 152.00 No Yes tt No Yes NASH-8-1 P. trichocarpa Nass 55.72 -128.82 183.00 No Yes tt No Yes NASH-8-4 P. trichocarpa Nass 55.72 -128.82 183.00 No Yes tt No Yes NASH-8-5 P. trichocarpa Nass 55.72 -128.82 183.00 Yes (pure) Yes tt No Yes NBON-29-1 P. trichocarpa Columbia 45.58 -122.00 300.00 No Yes NA No No NBON-29-2 P. trichocarpa Columbia 45.58 -122.00 300.00 No Yes NA No No NBON-29-4 P. trichocarpa Columbia 45.58 -122.00 300.00 No Yes NA No No NECA-14-1 P. trichocarpa Nechako 54.10 -124.43 655.00 Yes (pure) Yes tt No No NECB-14- P. trichocarpa Nechako 53.95 -124.43 671.00 Yes (pure) Yes tt 3 No   6 NHTB-27-2 P. trichocarpa Fraser 49.97 -121.82 335.00 No Yes NA No No NHTB-27-5 P. trichocarpa Fraser 49.97 -121.82 335.00 No Yes NA No No NKND-3-2 P. trichocarpa Taku 58.93 -133.18 122.00 Yes (admixed) Yes tt No Yes NPLN-30-3 P. trichocarpa Willamette 45.57 -123.00 100.00 No Yes NA No No NPLN-30-4 P. trichocarpa Willamette 45.57 -123.00 100.00 No Yes NA No No NPLN-30-5 P. trichocarpa Willamette 45.57 -123.00 100.00 No Yes NA No No PHLA-22-1 P. trichocarpa Philips 50.60 -125.32 5.00 Yes (pure) Yes NA No No PHLA-22-2 P. trichocarpa Philips 50.60 -125.32 5.00 No Yes NA No No PHLA-22-3 P. trichocarpa Philips 50.60 -125.32 5.00 No Yes NA No No PHLA-22-4 P. trichocarpa Philips 50.60 -125.32 5.00 No Yes NA No No PHLA-22-5 P. trichocarpa Philips 50.60 -125.32 5.00 No Yes NA No No PHLC-22-1 P. trichocarpa Philips 50.68 -125.25 58.00 No Yes NA No No PHLC-22-2 P. trichocarpa Philips 50.68 -125.25 58.00 No Yes NA No No PHLC-22-3 P. trichocarpa Philips 50.68 -125.25 58.00 No Yes NA No No PHLC-22-4 P. trichocarpa Philips 50.68 -125.25 58.00 No Yes NA No No PHLC-22-5 P. trichocarpa Philips 50.68 -125.25 58.00 No Yes NA No No PITS-29-1 P. trichocarpa Columbia 45.83 -123.12 900.00 No Yes NA No No PITS-29-2 P. trichocarpa Columbia 45.83 -123.12 900.00 No Yes NA No No PITS-29-3 P. trichocarpa Columbia 45.83 -123.12 900.00 No Yes NA No No PITS-29-4 P. trichocarpa Columbia 45.83 -123.12 900.00 No Yes NA No No   PITS-29-5 P. trichocarpa Columbia 45.83 -123.12 900.00 No Yes NA No No QAUS-16-1 P. trichocarpa Quesnel 52.72 -122.47 442.00 No Yes bt No Yes QAUS-16-3 P. trichocarpa Quesnel 52.72 -122.47 442.00 Yes (admixed) Yes bb 2 Yes QAUS-16-4 P. trichocarpa Quesnel 52.72 -122.47 442.00 No Yes bt No Yes QAUS-16-7 P. trichocarpa Quesnel 52.72 -122.47 442.00 No Yes bt No Yes QBKR-16-2 P. trichocarpa Quesnel 52.95 -122.87 823.00 No Yes tt 2 Yes QBKR-16-3 P. trichocarpa Quesnel 52.95 -122.87 823.00 Yes (admixed) Yes bt 2 Yes QBKR-16-4 P. trichocarpa Quesnel 52.95 -122.87 823.00 Yes (admixed) Yes tt 2 Yes QBKR-16-5 P. trichocarpa Quesnel 52.95 -122.87 823.00 Yes (admixed) Yes bt No Yes QCTN-16-1 P. trichocarpa Quesnel 53.03 -122.15 823.00 No Yes bt 2 Yes QCTN-16-3 P. trichocarpa Quesnel 53.03 -122.15 823.00 No Yes tt No Yes QCTN-16-4 P. trichocarpa Quesnel 53.03 -122.15 823.00 No Yes tt 2 Yes QFRS-16-1 P. trichocarpa Quesnel 53.07 -122.52 472.00 No Yes bt 2 Yes QFRS-16-2 P. trichocarpa Quesnel 53.07 -122.52 472.00 No Yes tt No Yes QFRS-16-3 P. trichocarpa Quesnel 53.07 -122.52 472.00 Yes (admixed) Yes bt No Yes QFRS-16-4 P. trichocarpa Quesnel 53.07 -122.52 472.00 Yes (admixed) Yes bt No Yes QFRS-16-5 P. trichocarpa Quesnel 53.07 -122.52 472.00 Yes (admixed) Yes tt 2 Yes QLKE-16-1 P. trichocarpa Quesnel 52.97 -122.32 488.00 Yes (admixed) Yes bt 2 Yes QLKE-16-2 P. trichocarpa Quesnel 52.97 -122.32 488.00 Yes (admixed) Yes tt No Yes   QLKE-16-3 P. trichocarpa Quesnel 52.97 -122.32 488.00 Yes (admixed) Yes tt 2 Yes QLKE-16-4 P. trichocarpa Quesnel 52.97 -122.32 488.00 No Yes tt 2 Yes SHEL-15-1 P. trichocarpa McGregor 54.03 -122.60 564.00 Yes (admixed) Yes bb 2 Yes SHEL-15-2 P. trichocarpa McGregor 54.03 -122.60 564.00 No Yes bt No Yes SHEL-15-3 P. trichocarpa McGregor 54.03 -122.60 564.00 Yes (admixed) Yes bb No Yes SHEL-15-4 P. trichocarpa McGregor 54.03 -122.60 564.00 Yes (admixed) Yes bb 2 Yes SHEL-15-5 P. trichocarpa McGregor 54.03 -122.60 564.00 No Yes tt 2 Yes SHEL-15-6 P. trichocarpa McGregor 54.03 -122.60 564.00 Yes (admixed) Yes tt No Yes SKNB-10-1 P. trichocarpa Skeena 54.68 -128.38 122.00 No Yes tt No Yes SKNB-10-2 P. trichocarpa Skeena 54.68 -128.38 122.00 No Yes tt No Yes SKNC-10-1 P. trichocarpa Skeena 54.77 -128.27 122.00 No Yes tt No Yes SKNC-10-2 P. trichocarpa Skeena 54.77 -128.27 122.00 No Yes tt 2 Yes SKNC-10-4 P. trichocarpa Skeena 54.77 -128.27 122.00 No Yes tt No Yes SKND-10-2 P. trichocarpa Skeena 54.85 -128.33 140.00 Yes (pure) Yes tt No Yes SKNL-10-1 P. trichocarpa Skeena 54.45 -128.75 61.00 No Yes tt No Yes SKNL-10-3 P. trichocarpa Skeena 54.45 -128.75 61.00 No Yes tt No Yes SKNL-10-4 P. trichocarpa Skeena 54.45 -128.75 61.00 No Yes tt No Yes SKNM-10-1 P. trichocarpa Skeena 54.40 -128.98 43.00 Yes (pure) Yes tt No Yes SKNM-10-2 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNM-10- P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes   3 SKNM-10-5 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No No SKNM-10-6 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNN-10-2 P. trichocarpa Skeena 54.40 -128.98 43.00 Yes (pure) Yes tt 2 Yes SKNN-10-3 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes bt No Yes SKNN-10-4 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNN-10-5 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNO-10-2 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNO-10-3 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNO-10-4 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNP-10-10 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No No SKNP-10-11 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNP-10-2 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNP-10-3 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNP-10-4 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes SKNP-10-8 P. trichocarpa Skeena 54.40 -128.98 43.00 Yes (pure) Yes tt 4 Yes SKNP-10-9 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt 4 Yes SKNQ-10-1 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No No SKNQ-10-3 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No Yes   SKNQ-10-4 P. trichocarpa Skeena 54.40 -128.98 43.00 No Yes tt No No SKNR-10-1 P. trichocarpa Skeena 54.68 -128.35 244.00 No Yes tt No Yes SKWB-24-4 P. trichocarpa Jervis 50.23 -124.00 115.00 No Yes NA No No SKWC-24-3 P. trichocarpa Jervis 50.25 -124.00 152.00 No Yes NA No No SKWC-24-4 P. trichocarpa Jervis 50.25 -124.00 152.00 No Yes NA No No SKWF-24-2 P. trichocarpa Jervis 50.25 -123.93 244.00 No Yes NA No No SLMD-28-5 P. trichocarpa Vancouver Island 50.28 -125.87 30.00 No Yes NA No No SQMA-25-3 P. trichocarpa Squamish 49.87 -123.23 61.00 No Yes NA No No SQMA-25-5 P. trichocarpa Squamish 49.87 -123.23 61.00 No Yes NA No No SQMC-25-1 P. trichocarpa Squamish 50.10 -123.37 177.00 Yes (pure) No NA No No SQMC-25-2 P. trichocarpa Squamish 50.10 -123.37 177.00 No Yes NA No No STEL-14-1 P. trichocarpa Nechako 54.03 -124.92 701.00 Yes (admixed) Yes bt No Yes STHA-21-2 P. trichocarpa Homathko 50.82 -124.48 239.00 No Yes NA No No STHA-21-3 P. trichocarpa Homathko 50.82 -124.48 239.00 No Yes NA No No STHA-21-4 P. trichocarpa Homathko 50.82 -124.48 239.00 No Yes NA No No STHA-21-5 P. trichocarpa Homathko 50.82 -124.48 239.00 No Yes NA No No STHB-21-1 P. trichocarpa Homathko 50.88 -124.73 91.00 No Yes NA No No STHB-21-2 P. trichocarpa Homathko 50.88 -124.73 91.00 No Yes NA No No STHB-21- P. trichocarpa Homathko 50.88 -124.73 91.00 No Yes NA No No   3 STHB-21-4 P. trichocarpa Homathko 50.88 -124.73 91.00 No Yes NA No No STHB-21-5 P. trichocarpa Homathko 50.88 -124.73 91.00 No Yes NA No No STKB-5-3 P. trichocarpa Lower Stikine 56.93 -131.78 31.00 No Yes bb No No STKB-5-4 P. trichocarpa Lower Stikine 56.93 -131.78 31.00 Yes (admixed) Yes bb No Yes STKD-5-1 P. trichocarpa Lower Stikine 57.33 -131.78 49.00 No Yes tt No Yes STKD-5-3 P. trichocarpa Lower Stikine 57.33 -131.78 49.00 No Yes bt No Yes STKE-5-3 P. trichocarpa Lower Stikine 57.52 -131.78 61.00 No Yes bb No Yes STKF-5-1 P. trichocarpa Lower Stikine 57.65 -131.57 85.00 Yes (admixed) Yes bt No Yes STKG-4-4 P. trichocarpa Upper Stikine 57.95 -129.67 732.00 No Yes tt No Yes TAKA-3-1 P. trichocarpa Taku 58.60 -133.57 31.00 No Yes bt No No TAKA-3-2 P. trichocarpa Taku 58.60 -133.57 31.00 No Yes tt No No TAKA-3-3 P. trichocarpa Taku 58.60 -133.57 31.00 No Yes tt No Yes TAKB-3-3 P. trichocarpa Taku 58.70 -133.40 49.00 Yes (admixed) Yes tt No Yes TAKB-3-4 P. trichocarpa Taku 58.70 -133.40 49.00 Yes (admixed) Yes bt No Yes TAKB-3-5 P. trichocarpa Taku 58.70 -133.40 49.00 Yes (admixed) Yes bt No Yes TATB-1-4 P. trichocarpa Alsek 59.43 -137.83 34.00 Yes (admixed) Yes bt No Yes TATB-1-7 P. trichocarpa Alsek 59.43 -137.83 34.00 Yes (admixed) Yes bt No Yes TLKH-11-1 P. trichocarpa Bulkley 54.67 -127.12 567.00 No Yes tt No Yes TLKH-11-5 P. trichocarpa Bulkley 54.67 -127.12 567.00 Yes (pure) Yes tt 2 Yes TLKI-11-1 P. trichocarpa Bulkley 54.67 -127.12 567.00 No Yes tt No No TNZA-4-3 P. trichocarpa Upper Stikine 58.30 -130.47 567.00 Yes (pure) Yes bb 2 Yes TOBA-23-2 P. trichocarpa Toba 50.52 -124.23 67.00 No Yes NA No No TOBA-23- P. trichocarpa Toba 50.52 -124.23 67.00 No Yes NA No No   3 TOBA-23-4 P. trichocarpa Toba 50.52 -124.23 67.00 No Yes NA No No TOBA-23-5 P. trichocarpa Toba 50.52 -124.23 67.00 No Yes NA No No TOBB-23-2 P. trichocarpa Toba 50.57 -124.08 73.00 No Yes NA No No TOBB-23-3 P. trichocarpa Toba 50.57 -124.08 73.00 No Yes NA No No TOBB-23-4 P. trichocarpa Toba 50.57 -124.08 73.00 No Yes NA No No TOBB-23-5 P. trichocarpa Toba 50.57 -124.08 73.00 No Yes NA No No TRTB-7-5 P. trichocarpa Bell-Irving 56.57 -129.82 640.00 No Yes bt No Yes TRTB-7-6 P. trichocarpa Bell-Irving 56.57 -129.82 640.00 No Yes tt No Yes TRTB-7-7 P. trichocarpa Bell-Irving 56.57 -129.82 640.00 No Yes tt No Yes WELC-27-3 P. trichocarpa Fraser 49.67 -121.42 91.00 Yes (pure) No NA No No WFSH-13-6 P. trichocarpa Stuart 54.60 -124.77 686.00 Yes (admixed) Yes tt No Yes WHTE-28-2 P. trichocarpa Vancouver Island 50.13 -126.05 213.00 No Yes NA No No WHTE-28-5 P. trichocarpa Vancouver Island 50.13 -126.05 213.00 No Yes NA No No WLOW-15-1 P. trichocarpa McGregor 53.92 -122.28 640.00 No Yes bt No Yes WLOW-15-3 P. trichocarpa McGregor 53.92 -122.28 640.00 No Yes tt 2 Yes WLOW-15-4 P. trichocarpa McGregor 53.92 -122.28 640.00 No Yes tt No Yes WLOW-15-5 P. trichocarpa McGregor 53.92 -122.28 640.00 Yes (admixed) Yes bt No Yes YALD-27-3 P. trichocarpa Fraser 49.57 -121.47 549.00 No Yes NA No No YALD-27-4 P. trichocarpa Fraser 49.57 -121.47 549.00 No Yes NA No No ZYMJ-10- P. trichocarpa Skeena 54.47 -127.93 305.00 No Yes tt No Yes   1 ZYMJ-10-5 P. trichocarpa Skeena 54.47 -127.93 305.00 No Yes tt 2 Yes     Table S2. Parameters for the RASPberry model with the highest log likelihood value, based on a whole genome SNP data set (see supplementary M&M) in 25 pure P. balsamifera, 25 pure P. trichocarpa and 68 admixed individuals. Parameter* Model defaultRate 5 //cM per Megabase timeSinceAdmixture 10 ancestryPropFile ** ancestralRate_tricho (Levsen)† 300 ancestralRate_balsamifera (Levsen)† 200 miscopyRate 0.05 mutation1 0.0079365 mutation2 0.0079365 miscopyMutation 0.01 recomputeWindowSize 2 collapsingDistance 3  *See Price et al 2009 and Wegmann et al 2011 **used whole genome stimation from 900K SNP data set which is highly correlated to that based on chromosome 6,12 and 15 using whole SNP scanning † Based on Levsen et al. 2012                  Table S3. Candidate genes for local adaptation across P. trichocarpa’s range, in chromosome 6 and 15 based on FST outlier tests and/or association analysis with environmental   variables and phenotypic traits (Geraldes et al. 2014; McKnown et al. 2014), and using a 34k SNP chip.  Selected candidates* Chr Gene modela Start kbb Annotationc Fst testd Geo/Env correlation teste Trait associa. testf Introgressed Region¶      Fdist Bayescan    Yes 6 Potri.006G020600 1448.9 FAR1  *** ***    Yes 6 Potri.006G020700 1454.7 FHY3 *** *** Lat,Long   No 6 Potri.006G048500 3475.9 Glycosyltransferase *** *** Lat,MAT,MCMT,DD_0,DD_18  A No 6 Potri.006G049700 3580.3 AP2 ***       A No 6 Potri.006G053800 3923.9 Zinc finger ** ** MWMT   A Yes 15 Potri.015G000200 12.7 ABCB19 ***    B Yes 15 Potri.015G000500 26.5 LSU4  **    B Yes 15 Potri.015G002300 137.8 PRR5  *** *** Lat,MAT,MCMT,TD,DD_0,DD_18,EMT Phenology - Biomass- Ecophysiology B Yes 15 Potri.015G002600 162.0 TTG1 *** *** Lat,MAT,MCMT,TD,DD_0,DD_18,EMT Phenology - Biomass- Ecophysiology B Yes 15 Potri.015G003100 236.7 COMT1 ***  Lat  B Yes 15 Potri.015G004100 276.7 NAC062 **  Lat,MCMT,TD,DD_0,EMT Phenology - Ecophysiology B Yes 15 Potri.015G006500 406.8 Unknown  *** *** Lat,MCMT,TD,DD_0,EMT  B Yes 15 Potri.015G009100 597.6 Yippee *** *** Lat,MCMT,DD_0 Phenology B Yes 15 Potri.015G009300 611.5 Dof- zinc finger ** *** Lat,MAT,MCMT,TD,DD_0,DD_18,EMT Phenology - Ecophysiology B No 15 Potri.015G125500 13870.2 MADS box       Phenology - Biomass C              Table S4. Quantitive reverse transcription PCR (qTt-PCR) to test the levels of expression of  COMT1 genes in different P. trichocarpa genotypes. Table S4A. Primers used in qRT-PCR Primer Sequence CO1-rt-F GTTGATGCCATAATGCTGGCACAT CO1-rt-R CACGTACGTATTGAATGCACAGCACATC 18S-F  AATTGTTGGTCTTCAACGAGGAA 18S-R  AAAGGGCAGGGACGTAGTCAA *For qRT-PCR analyses, 5 individuals from each poplar genotypes were randomly selected: homozygotes for balsamifera COMT1 (QQ), homozygotes for trichocarpa COMT1 (PP) and heterozygotes (QP). RNA was isolated from leaf tissue harvested on August 2013 from 11:00 am to 1:00 pm, following the protocol of Kolosova et al. (2004) (1). RNA was quantified based on absorption at 260 nm and then reverse-transcribed into cDNA using the SuperScript First-Strand Synthesis system (Invitrogen). Primers for the target gene (COMT1: CO1-rt-F, CO1-rt-R) were designed using Primer-Blast (2) and primers from for the reference gene (18S) were obtained from (3) (18S-F, 18S-R). Using all cDNA samples and three technical replicates per sample, we performed quantitative PCR using SYBR® Select Master Mix with CFX Connect™ Real-Time PCR Detection System (Invitrogen). To analyze gene expression levels, the 2∆CT method (4) was used. We subtracted the Ct (threshold cycle) value of the target gene (COMT1) by the Ct value of the reference housekeeping gene (18S) to standardize for the amounts of RNA template. Here, the larger the ∆CT value, the lower the mRNA level. The Ct values were then compared between genotype groups using ANOVA and multiple comparison Tukey test. We also converted ΔCT values to a linear form using the term 2–ΔCT.  Table S4B. Gene expression levels in different genotypes of COMT1 based on qRT-PCR. QQ represents genotypes homozygotes for P. balsamifera haplotypes, QP represents heterozygotes and PP represents genotypes homozygotes for P. trichocarpa haplotypes. Sample COMT1_Genotype Ct_18S_reference gene Ct_COMT1 ΔCT (Cq_COMT1 - Cq_18S)  2–ΔCT QQ22 QQ 15.94 27.73 11.80 0.000280444 QQ28 QQ 16.31 28.26 11.95 0.000252031 QQ25 QQ 18.37 28.51 10.14 0.000884204 QQ30 QQ 17.49 28.17 10.68 0.000610946 QQ23 QQ 15.27 27.33 12.06 0.000234737 QP27 PQ 14.9 27.03 12.13 0.000223103 QP14 PQ 16.00 27.92 11.92 0.000258061 QP44 PQ 14.57 27.40 12.83 0.000137654 QP8 PQ 17.22 30.14 12.92 0.000128733 QP9 PQ 15.47 28.37 12.90 0.00013053 PP2 PP 13.88 28.28 14.40 4.64E-05 PP26 PP 14.15 28.47 14.32 4.89E-05 PP35 PP 13.59 26.89 13.30 9.89E-05 PP5 PP 13.28 28.17 14.89 3.29E-05 PP6 PP 13.69 27.53 13.84 6.84E-05   Table S5. List of genes in introgressed region from chromosome 6 and 15 based on local ancestry analysis in RASPberry. Gene model v3 Chromosome Introgressed Region (see Figure 2) Start bp Potri.006G047300 6 A 3362926 Potri.006G047400 6 A 3367842 Potri.006G047500 6 A 3382904 Potri.006G047600 6 A 3387931 Potri.006G047700 6 A 3394337 Potri.006G047800 6 A 3412602 Potri.006G047900 6 A 3416251 Potri.006G048000 6 A 3428314 Potri.006G048100 6 A 3435767 Potri.006G048200 6 A 3441197 Potri.006G048300 6 A 3453082 Potri.006G048400 6 A 3455995 Potri.006G048500 6 A 3476876 Potri.006G048600 6 A 3479534 Potri.006G048700 6 A 3494410 Potri.006G048800 6 A 3502417 Potri.006G048900 6 A 3511577 Potri.006G049000 6 A 3516210 Potri.006G049100 6 A 3518027 Potri.006G049200 6 A 3534435 Potri.006G049300 6 A 3539405 Potri.006G049400 6 A 3572786 Potri.006G049500 6 A 3575352 Potri.006G049600 6 A 3577659 Potri.006G049700 6 A 3580290 Potri.006G049800 6 A 3584244 Potri.006G049900 6 A 3585352 Potri.006G050000 6 A 3590598 Potri.006G050100 6 A 3612871 Potri.006G050200 6 A 3620003 Gene model v3 Chromosome Introgressed Region (see Figure 2) Start bp Potri.006G050300 6 A 3643063 Potri.006G050400 6 A 3648901 Potri.006G050500 6 A 3650962 Potri.006G050600 6 A 3652919 Potri.006G050700 6 A 3655561 Potri.006G050800 6 A 3666733 Potri.006G050900 6 A 3672741 Potri.006G051000 6 A 3681915 Potri.006G051100 6 A 3686833 Potri.006G051200 6 A 3693920 Potri.006G051300 6 A 3700986 Potri.006G051400 6 A 3706602 Potri.006G051500 6 A 3708051 Potri.006G051600 6 A 3712940 Potri.006G051700 6 A 3723120 Potri.006G051800 6 A 3728291 Potri.006G051900 6 A 3732757 Potri.006G052000 6 A 3734407 Potri.006G052100 6 A 3736693 Potri.006G052200 6 A 3749410 Potri.006G052300 6 A 3756829 Potri.006G052400 6 A 3760125 Potri.006G052500 6 A 3768101 Potri.006G052600 6 A 3768788 Potri.006G052700 6 A 3778059 Potri.006G052800 6 A 3786821 Potri.006G052900 6 A 3811387 Potri.006G053000 6 A 3824895 Potri.006G053100 6 A 3831484 Potri.006G053200 6 A 3841284   Potri.006G053300 6 A 3854946 Potri.006G053400 6 A 3875357 Potri.006G053500 6 A 3886219 Potri.006G053600 6 A 3899010 Potri.006G053700 6 A 3901982 Potri.006G053800 6 A 3923944 Potri.006G053900 6 A 3934404 Potri.015G000100 15 B 718 Potri.015G000200 15 B 12677 Potri.015G000300 15 B 18076 Potri.015G000400 15 B 21154 Potri.015G000500 15 B 26481 Potri.015G000600 15 B 32239 Potri.015G000700 15 B 37947 Potri.015G000800 15 B 40286 Potri.015G000900 15 B 42652 Potri.015G001000 15 B 62625 Potri.015G001100 15 B 70823 Potri.015G001200 15 B 72405 Potri.015G001300 15 B 76529 Potri.015G001400 15 B 84957 Potri.015G001500 15 B 95829 Potri.015G001600 15 B 106143 Potri.015G001700 15 B 113349 Potri.015G001800 15 B 119245 Potri.015G001900 15 B 120496 Potri.015G002000 15 B 125378 Potri.015G002100 15 B 126927 Potri.015G002200 15 B 133318 Potri.015G002300 15 B 137759 Potri.015G002400 15 B 146190 Potri.015G002500 15 B 149764 Potri.015G002600 15 B 162021 Potri.015G002700 15 B 169831 Potri.015G002800 15 B 183196 Potri.015G002900 15 B 203640 Potri.015G003000 15 B 209639 Potri.015G003100 15 B 236968 Potri.015G003200 15 B 240398 Potri.015G003300 15 B 244282 Potri.015G003400 15 B 246736 Potri.015G003500 15 B 247166 Potri.015G003600 15 B 251085 Potri.015G003700 15 B 253596 Potri.015G003800 15 B 262782 Potri.015G003900 15 B 268522 Potri.015G004000 15 B 273252 Potri.015G004100 15 B 276664 Potri.015G004200 15 B 281188 Potri.015G004300 15 B 289125 Potri.015G004400 15 B 292701 Potri.015G004500 15 B 297501 Potri.015G004600 15 B 301982 Potri.015G004700 15 B 310478 Potri.015G004800 15 B 313921 Potri.015G004900 15 B 317586 Potri.015G005000 15 B 318346 Potri.015G005100 15 B 324815 Potri.015G005200 15 B 329951 Potri.015G005300 15 B 334725 Potri.015G005400 15 B 342635 Potri.015G005500 15 B 349201 Potri.015G005600 15 B 355168 Potri.015G005700 15 B 360375 Potri.015G005800 15 B 362192 Potri.015G005900 15 B 367350 Potri.015G006000 15 B 375417 Potri.015G006100 15 B 388134   Potri.015G006200 15 B 394635 Potri.015G006300 15 B 401359 Potri.015G006400 15 B 404468 Potri.015G006500 15 B 406777 Potri.015G006600 15 B 409935 Potri.015G006700 15 B 412188 Potri.015G006800 15 B 422668 Potri.015G006900 15 B 440386 Potri.015G007000 15 B 444823 Potri.015G007100 15 B 448365 Potri.015G007200 15 B 452861 Potri.015G007300 15 B 458876 Potri.015G007400 15 B 466963 Potri.015G007500 15 B 472570 Potri.015G007600 15 B 474256 Potri.015G007700 15 B 480884 Potri.015G007800 15 B 488522 Potri.015G007900 15 B 491967 Potri.015G008000 15 B 494511 Potri.015G008100 15 B 502912 Potri.015G008200 15 B 507230 Potri.015G008300 15 B 521697 Potri.015G008400 15 B 526505 Potri.015G008500 15 B 527335 Potri.015G008600 15 B 549477 Potri.015G008700 15 B 571152 Potri.015G008800 15 B 585592 Potri.015G008900 15 B 590801 Potri.015G009000 15 B 592354 Potri.015G009100 15 B 597610 Potri.015G009200 15 B 601409 Potri.015G009300 15 B 611499 Potri.015G009400 15 B 621712 Potri.015G009500 15 B 629684 Potri.015G009600 15 B 640314 Potri.015G009700 15 B 655882 Potri.015G009800 15 B 659824 Potri.015G009900 15 B 665491 Potri.015G010000 15 B 670429 Potri.015G010100 15 B 673363 Potri.015G010200 15 B 679470 Potri.015G010300 15 B 686701 Potri.015G010400 15 B 692700 Potri.015G010500 15 B 703077 Potri.015G010600 15 B 707479 Potri.015G010700 15 B 710140 Potri.015G010800 15 B 713815 Potri.015G010900 15 B 721815 Potri.015G011000 15 B 725856 Potri.015G011100 15 B 729257 Potri.015G011200 15 B 735325 Potri.015G011300 15 B 742773 Potri.015G011400 15 B 745998 Potri.015G011500 15 B 753082 Potri.015G011600 15 B 754817 Potri.015G011700 15 B 756920 Potri.015G011800 15 B 758283 Potri.015G011900 15 B 761676 Potri.015G012000 15 B 765908 Potri.015G012100 15 B 775679 Potri.015G012200 15 B 780352 Potri.015G012300 15 B 787447 Potri.015G012400 15 B 792937 Potri.015G012500 15 B 804149 Potri.015G012600 15 B 814410 Potri.015G012700 15 B 823142 Potri.015G012800 15 B 829009 Potri.015G012900 15 B 840198   Potri.015G013000 15 B 849511 Potri.015G013100 15 B 859616 Potri.015G013200 15 B 866349 Potri.015G013300 15 B 869556 Potri.015G013400 15 B 879297 Potri.015G118500 15 C 13340589 Potri.015G118600 15 C 13347602 Potri.015G118700 15 C 13358567 Potri.015G118800 15 C 13363254 Potri.015G118900 15 C 13378867 Potri.015G119000 15 C 13381315 Potri.015G119100 15 C 13384217 Potri.015G119200 15 C 13387137 Potri.015G119300 15 C 13388708 Potri.015G119400 15 C 13420539 Potri.015G119500 15 C 13427881 Potri.015G119600 15 C 13437147 Potri.015G119700 15 C 13443181 Potri.015G119800 15 C 13450146 Potri.015G119900 15 C 13495791 Potri.015G120000 15 C 13497065 Potri.015G120100 15 C 13500740 Potri.015G120200 15 C 13504131 Potri.015G120300 15 C 13513875 Potri.015G120400 15 C 13517154 Potri.015G120500 15 C 13524911 Potri.015G120600 15 C 13534933 Potri.015G120700 15 C 13538777 Potri.015G120800 15 C 13542174 Potri.015G120900 15 C 13543412 Potri.015G121000 15 C 13547456 Potri.015G121100 15 C 13555980 Potri.015G121200 15 C 13557989 Potri.015G121300 15 C 13565623 Potri.015G121400 15 C 13574575 Potri.015G121500 15 C 13583571 Potri.015G121600 15 C 13584454 Potri.015G121700 15 C 13588790 Potri.015G121800 15 C 13592871 Potri.015G121900 15 C 13604850 Potri.015G122000 15 C 13605985 Potri.015G122100 15 C 13609021 Potri.015G122200 15 C 13611137 Potri.015G122300 15 C 13618881 Potri.015G122400 15 C 13627969 Potri.015G122500 15 C 13635414 Potri.015G122600 15 C 13638401 Potri.015G122700 15 C 13639994 Potri.015G122800 15 C 13653311 Potri.015G122900 15 C 13660828 Potri.015G123000 15 C 13672157 Potri.015G123100 15 C 13683044 Potri.015G123200 15 C 13691247 Potri.015G123300 15 C 13696202 Potri.015G123400 15 C 13697565 Potri.015G123500 15 C 13707245 Potri.015G123600 15 C 13711820 Potri.015G123700 15 C 13729143 Potri.015G123800 15 C 13741366 Potri.015G123900 15 C 13749090 Potri.015G124000 15 C 13752932 Potri.015G124100 15 C 13757991 Potri.015G124200 15 C 13767796 Potri.015G124300 15 C 13781891 Potri.015G124400 15 C 13798542 Potri.015G124500 15 C 13806271 Potri.015G124600 15 C 13824535 Potri.015G124700 15 C 13829810   Potri.015G124800 15 C 13834878 Potri.015G124900 15 C 13840486 Potri.015G125000 15 C 13841314 Potri.015G125100 15 C 13848997 Potri.015G125200 15 C 13854295 Potri.015G125300 15 C 13855993 Potri.015G125400 15 C 13861692 Potri.015G125500 15 C 13870204 Potri.015G125600 15 C 13874217 Potri.015G125700 15 C 13878009 Potri.015G125800 15 C 13884264 Potri.015G125900 15 C 13887037 Potri.015G126000 15 C 13889098 Potri.015G126100 15 C 13892764 Potri.015G126200 15 C 13893781 Potri.015G126300 15 C 13897845 Potri.015G126400 15 C 13898667 Potri.015G126500 15 C 13904779 Potri.015G126600 15 C 13907143 Potri.015G126700 15 C 13910051 Potri.015G126800 15 C 13913898   Table S6. A  Introgressed genes from P. balsamifera in P. trichocarpa in a telomeric region of chromosome 15, corresponding Arabidopsis ortholog gene code, GO term or protein group enriched in the introgressed regions, Tajima's D values higher than 99% of the distribution, genes with significant positive values of alpha and nucleotide diversity values higher than 95% of the distribution in P. balsamifera  Gene model v3 Description start end Arabidopsis best hit GO term enriched Tajima's D Positive selection (alpha)* Pi-balsamifera Potri.015G000100 VIT family 718 7519   Tajima > 99%  Potri.015G000200 ABCB19; ATPase, coupled to transmembrane movement of substances / auxin efflux transmembrane transporter 12677 18022 AT3G28860 GO:0048466;GO:0048443;SM00382:AAA;GO:0016887;IPR003593;GO:0010218;; Tajima > 99%  Potri.015G000300 Peptidase family C78, Uncharacterized conserved protein 18076 20078   Tajima > 99%  Potri.015G000400 Autophagy-related protein 13, Phosphoprotein involved in cytoplasm to vacuole targeting and autophagy 21154 24866   Tajima > 99%    Potri.015G000500 NA- Ath 50% ~LSU4 response to low sulfur 4, similar to expressed protein in Arabidopsis thaliana%3B [ co-ortholog (2of2) of At3g49580 C At5g24655 C At5g24660 C At3g49570 C ] 26481 27392   Tajima > 99%  Potri.015G000600 mitochondrial import inner membrane translocase subunit Tim17 FTim22 FTim23 family protein%3B [ co-ortholog (1of2) of At3g49560 C At5g24650 C ] 32239 35641   Tajima > 99%  Potri.015G000700 NA* 37947 40110   Tajima > 99%  Potri.015G000800 Thaumatin-like protein  (Arabidopsis thaliana) GI:2435406  [ co-ortholog (1of2) of At5g24620 C ] 40286 41854   Tajima > 99%  Potri.015G000900 NA 42652 45307   Tajima > 99%  Potri.015G001000 Rpp14/Pop5 family RNase P/RNase MRP subunit POP5 LIPOATE-PROTEIN LIGASE B 62625 64009   Tajima > 99% Pi > 95% Potri.015G001100 Unknown function, DUF599 -At5g24600 C ] 70823 71165   Tajima > 99% Pi > 95%   Potri.015G001200 Rpp14 family protein3B ribonuclease P family protein At1g04635 C ] 72405 76263 AT1G04635 GO:0006396;GO:0043228;GO:0043232;GO:0070013;GO:0043233;GO:0031981;GO:0031974; Tajima > 99% Pi > 95% Potri.015G001300 Protein of unknown function, DUF599 -At5g24600 C ] 76529 77962   Tajima > 99% Pi > 95% Potri.015G001400 NA 84957 85645   Tajima > 99% Pi > 95% Potri.015G001500 Protein of unknown function, DUF599 -At5g24600 C ] 95829 97634   Tajima > 99% Pi > 95% Potri.015G001600 Rpp14/Pop5 family, LIPOATE-PROTEIN LIGASE B, ribonuclease activity 106143 107360   Tajima > 95% Pi > 95% Potri.015G001700 NA& 113349 114150   Tajima > 95% Pi > 95% Potri.015G001800 NA 119245 120097   Tajima > 95% Pi > 95% Potri.015G001900 SPFH stomatin-like band 7 family protein HFLC Prohibitins and stomatins of the PID superfamily 120496 124220   Tajima > 95% Pi > 95% Potri.015G002000 NA 125378 125545   Tajima > 95% Pi > 95% Potri.015G002100  F-box domain 126927 130749   Tajima > 95% Pi > 95% Potri.015G002200 Sigma 54 modulation protein / S30EA ribosomal protein 133327 136045 AT5G24490 GO:0043228;GO:0043232; Tajima > 95% Pi > 95% Potri.015G002300 PRR5 PSEUDO-RESPONSE REGULATOR 5%3B [ co-ortholog (2of3) of At5g24470 C ] 137759 143403 AT5G24470 GO:0010218; Tajima > 95% Pi > 95%   Potri.015G002400 Late embryogenesis abundant protein 146192 147599   Tajima > 95% Pi > 95% Potri.015G002500 NA 149764 151121   Tajima > 95% Pi > 95% Potri.015G002600 TTG1, TRANSPARENT TESTA GLABRA 1, TTG, TTG1, UNARMED 23, URM23 162021 163539      Potri.015G002700 NA 169831 169932      Potri.015G002800 2OG-Fe(II) oxygenase superfamily, oxidoreductases 183196 190645    x Pi < 5% Potri.015G002900 NAC147 No apical meristem 203640 204896 AT1G71930 IPR003441;  x Pi < 5% Potri.015G003000 nuclear RNA polymerase C2 209639 235482    x Pi < 5% Potri.015G003100 COMT1  similar to Chain A%3B similar to Crystal Structure Analysis Of Caffeic Acid5-Hydroxyferulic Acid 35-O-Methyltransferase Ferulic Acid Complex. [ORG:Medicago sativa]%3B [ co-ortholog (2of2) of CAA58218 C 1KYW_C C 1KYZ_A C At5g54160 C ] 236720 239777    x Pi < 5% Potri.015G003200 NA^ 240398 242448    x Pi < 5%   Potri.015G003300 NAC-UBA/TS-N domain, NASCENT POLYPEPTIDE ASSOCIATED COMPLEX ALPHA SUBUNIT-RELATED 244282 246269    x Pi < 5% Potri.015G003400 NA 246736 247092    x Pi < 5% Potri.015G003500 Peroxidase, oxidation reduction, heme binding, response to oxidative stress 247166 249255    x Pi < 5% Potri.015G003600 Peroxidase, oxidation reduction, heme binding, response to oxidative stress 251085 252707    x Pi < 5% Potri.015G003700 NA# 253596 259375    x Pi < 5% Potri.015G003800 copper-binding protein-related%3B similar to low similarity to copper homeostasis factor gi:3168840 from Arabidopsis thaliana%3B [ co-ortholog (1of2) of At4g27590 C ] 262782 264158    x Pi < 5%   Potri.015G003900 copper-binding family protein%3B similar to copper homeostasis factor gi:3168840 from Arabidopsis thaliana%3B copper-binding family protein%3B similar to copper homeostasis factor gi:3168840 from Ara%3B [ co-ortholog (2of2) of At5g24580 C ] 268522 271061    x Pi < 5% Potri.015G004000 Peptidase family M20/M25/M40, IAA-amino acid hydrolase 272966 276146    x Pi < 5% Potri.015G004100 anac062 (NAC62); TF 276664 279681 AT3G49530 IPR003441;   x Pi < 5% *Alpha estimates of a region comprising 14 genes within a 110-kb region (from 183 kb to 280 kb in chromosome 15) revealed signals of positive selection in 46% and 41% of all amino acid substitutions in P. trichocarpa and P. balsamifera respectively                     Table S6B Genes from 280 kb to 880 kb from region B in chromosome 15 and region A in chromosome 6 associated with GO terms and protein groups enriched in the introgressed regions from P.balsamifera into P. trichocarpa.  Gene model v3   Description start Arabidopsis best hit GO enriched Potri.015G004300 Unknown function, DUF623  289125 AT4G18830 GO:0031981;GO:0031974;GO:0043228;GO:0043232;GO:0070013;GO:0043233; Potri.015G004600 RNA recognition motif (RRM, RBD,RNP domain) Alternative splicing factor ASF/SF2 (RRM superfamily) 301982 AT3G49430 GO:0031981;GO:0031974;GO:0006396;GO:0043228;GO:0043232;GO:0070013;GO:0043233 Potri.015G004700 60S acidic ribosomal protein P1.%3B [ co-ortholog (2of2) of At4g00810 C At5g47700 C At1g01100 C ] 310478 AT5G24510 GO:0043228;GO:0043232; Potri.015G005200 similar to mitochondrial transcription termination factor-related%3B similar to mTERF-related%3B [ co-ortholog (1of2) of At5g54180 C ] 329951 AT5G54180 GO:0043228;GO:0043232; Potri.015G006000   375417 AT3G53480 IPR003593;SM00382:AAA;GO:0016887 Potri.015G006200 QLQ regulation of transcription, DNA-dependent in Ath  growth-regulating factor 7 394635 AT5G53660 GO:0010218 Potri.015G006300  401359 AT5G51660 GO:0006396 Potri.015G007000 No apical meristem (NAM) protein 444823 AT5G17260 IPR003441 Potri.015G007100 UBIQUITIN EXTENSION PROTEIN 1%3B [ co-ortholog (2of4) of At3g52590 C At2g36170 C ] 448365 AT3G52590 GO:0031981;GO:0031974;GO:0043228;GO:0043232;GO:0070013;GO:0043233;   Potri.015G007700 MSP1 protein%3B putative%3B similar to intramitochondrial sorting protein%3B putative%3B similar to Swiss-Prot:P28737 MSP1 protein (TAT-binding homolog 4) (Saccharomyces cerevisiae)%3B similar to AAA family%3B [ co-ortholog (1of5) of At4g27680 C At5g53540 C 480884 AT4G27680 IPR003593;SM00382:AAA;GO:0016887 Potri.015G007800  488522 AT2G46620 IPR003593;SM00382:AAA;GO:0016887 Potri.015G008700 similar to RNA helicase%3B putative%3B similar to SP%7CQ14562%7CATP dependent-helicase DDX8 RNA (helicase HRH1 DEAH) (box-protein 8 %7BHomo) %7Bsapiens%7D %3B [ ortholog of At1g32490 CAt4g16680 CAt2g35340 C] 571152 AT1G32490 GO:0006396;GO:0016887; Potri.015G009100 Yippee putative zinc-binding protein 597610 AT4G27740 PIRSF028804 Potri.015G009200 Yippee-like protein At4g27740.%3B [ co-ortholog (2of5) of At4g27740 C ], FAD NAD BINDING OXIDOREDUCTASES 601409 AT4G27745 PIRSF028804 Potri.015G009600 PHD finger family protein%3B similar to SET domain-containing protein%3B [ co-ortholog (2of2) of At5g24330 C ] 640314 AT5G24330 GO:0048466;GO:0048443; Potri.015G009900  665491 AT5G53490.3 GO:0070013;GO:0043233;GO:0031974 Potri.015G010600 similar to Protein phosphatase 2C PPH1 (EC 3.36) (PP2C).%3B [ ortholog of At4g27800 C] 707479 AT4G27800 GO:0043228;GO:0043232;GO:0031981;GO:0031974;GO:0070013;GO:0043233; Potri.015G010700   710140 AT5G24314 GO:0043228;GO:0043232; Potri.015G012900  840198 AT5G53350 IPR003593;GO:0070013;GO:0043233;GO:0031974;SM00382:AAA;GO:0016887; Potri.006G045300 PF00240-Ubiquitin family 3200269 AT3G52590 GO:0031981;GO:0031974;GO:0043228;GO:0043232;;; Potri.006G048000 PF00154-recA bacterial DNA recombination protein 3428314 AT3G10140 IPR003593;SM00382:AAA;GO:0016887 Potri.006G048300 PF00076-RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 3453082 AT1G51510 GO:0006396;GO:0043228;GO:0043232;GO:0031981;GO:0031974;GO:0070013;GO:0043233 Potri.006G048400 PF08271-TFIIB zinc-binding;PF00382-Transcription factor TFIIB repeat 3455995 AT3G10330 GO:0070013;GO:0043233;GO:0031981;GO:0031974;;;   Potri.006G048600 PF00225-Kinesin motor domain;PF00307-Calponin homology (CH) domain 3479534 AT3G10310 GO:0043228;GO:0043232; Potri.006G049000  3516210 AT3G21090 IPR003593;SM00382:AAA;GO:0016887 Potri.006G049300 PF00005-ABC transporter 3539405 AT2G41700 GO:0016887 Potri.006G050200 PF00626-Gelsolin repeat;PF02209-Villin headpiece domain 3620003 AT2G41740 GO:0043228;GO:0043232; Potri.006G051200 PF01138-3' exoribonuclease family, domain 1 3693920 AT1G60080 GO:0006396 Potri.006G051300 PF10288-Protein of unknown function (DUF2392) 3700986 AT4G35910 GO:0006396 Potri.006G051400 PF02365-No apical meristem (NAM) protein 3706602 AT3G04070 IPR003441 Potri.006G052400 PF03719-Ribosomal protein S5, C-terminal domain;PF00333-Ribosomal protein S5, N-terminal domain 3760125 AT3G57490 GO:0043228;GO:0043232; Potri.006G052700 PF00295-Glycosyl hydrolases family 28 3778059 AT3G07970 GO:0048466;GO:0048443; Potri.006G053500 PF02045-CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B 3886219 AT3G14020 GO:0031981;GO:0070013;GO:0043233;GO:0031974;;;  Supplementary Table 6C List of GO terms enriched in the introgressed regions from P. balsamifera into P. trichocarpa. GO:0006396~RNA processing GO:0010218~response to far red light GO:0016887~ATPase activity GO:0031974~membrane-enclosed lumen GO:0031981~nuclear lumen GO:0043228~non-membrane-bounded organelle GO:0043232~intracellular non-membrane-bounded organelle GO:0043233~organelle lumen GO:0048443~stamen development GO:0048466~androecium development GO:0070013~intracellular organelle lumen IPR003441:No apical meristem (NAM) protein IPR003593:ATPase, AAA+ type, core PIRSF028804:protein yippee-like SM00382:AAA     Table S7. List of genes in introgressed region B in chromosome 15 that showed significantly different levels of expression in admixed (bb, bt) individuals compared to pure P. trichocarpa individuals.    Anova Tukey tests   Anova Tukey tests Gene model v3 Description Leaf Mean FPKM F-value p-value *Leaf Expression Xylem Mean FPKM Fvalue pvalue *Xylem Expression Potri.015G001200 Major Facilitator Superfamily, ET TRANSLATION PRODUCT-RELATED, Uncharacterized conserved protein 9.577835 30.65 1.51E-10 tt>bt>bb 22.81604 31.62 2.33E-10 tt>bt=bb Potri.015G001500  0.07304318 15.42 2.28E-06 bb>bt=tt 0.002600863 ns ns  Potri.015G002100  F-box domain 13.62576 29.91 2.29E-10 tt>bt>bb 7.238503 29.7 6.31E-10 tt>bt>bb Potri.015G002600 TTG1, TRANSPARENT TESTA GLABRA 1, TTG, TTG1, UNARMED 23, URM23 18.45906 7.873 0.000768 bb=bt>tt 9.671041 50.61 4.74E-14 bb>bt>tt Potri.015G003100 COMT1 9.53016 72.54 <2e-16 bb>bt>tt 102.9831 72.48 <2e-16 bb>bt>tt Potri.015G003200  0.3963508 47.86 2.73E-14 bt>bb=tt 1.090179 ns ns  Potri.015G003800  0.1366683 14.23 5.39E-06 bt>tt 0.006370198 ns ns  Potri.015G004200 CCR4 Endonuclease/Exonuclease/phosphatase family, CARBON CATABOLITE REPRESSOR PROTEIN 4 1.341835 7.833 0.000794 bt=bb>tt 0.327882 52.36 2.39E-14 bb>bt>tt Potri.015G005900  0.1446214 21.76 3.09E-08 bt>bb=tt 0.01141833 ns ns  Potri.015G006000  0.01184041 6.481 0.00249 bt>bb=tt 0.007379346 10.67 9.67E-05 bt>bb=tt Potri.015G007200  28.90136 ns ns  51.09009 14.89 4.60E-06 bb>bt=tt Potri.015G011300  alpha/beta hydrolase fold,Soluble epoxide hydrolase 6.392737 7.771 0.000837 bb>tt 2.703451 12.2 3.11E-05 bb=bt>tt Potri.015G012300  4.513397 ns ns  9.047215 19.31 2.50E-07 bb>bt=tt Potri.015G012700  13.73239 12.19 2.47E-05 bt=bb>tt 17.03197 ns ns       *RNAseq data was obtained from developing xylem in 197 accessions (385 samples including replicates), and from expanding leaves of defined developmental stage in 191 accessions (389 samples including replicates) grown at Totem Field. For the nearly 800 samples, RNA-seq reads were mapped to the ~40,000 genes in the poplar reference genome, and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were estimated (Corea, et al. In preparation). We compared levels of gene expression (measured by FPKM values) among the three genotypic categories (bb, bt and tt) using ANOVAs correcting p-values for multiple testing. Among the 134 genes. : bb and bt represent admixed homozygotes and heterozygote genotypes for balsam alleles respectively. tt represents genotypes homozygotes for trichocarpa alleles. ns= pvalue >0.05                                   Table S8. A Genes from the first introgressed region of chromosome 15 that showed associations with traits related to phenology, ecophysiology and biomass (McKown et at. 2014)   Phenology Biomass Ecophysiology Gene model v3 Gene name Bud set Leaf drop Post-bud set period 100% Yellowing Growth period Height Height growth cessation Chlsummer Nmass Potri.015G002300 PRR5  x x x     x   x   Potri.015G002600 TTG1 x x x   x x x x   Potri.015G004100 ANAC062 x x   x x   x x x Potri.015G009100 Yippee               x   Potri.015G009300 Dof-type zinc finger x x x x x     x    Table S8. B. List of traits used in ANOVAs to determine if admixed individuals with balsamifera introgressed region are phenotypically different to those trichocarpa individuals without balsamifera genes. Chlsummer: Chlorophyll content summer, Nmass: Leaf nitrogen content per unit dry mass, Post.bud_set: Post bud set period, Yellowing_100%: total canopy leaf yellowing. The complete data set can be found in McKown et al. 2013 - Supporting information STable 2 Trait type Traits from 2008 Traits from 2009 Traits from 2010 Traits from 2011 Total datasets Phenology Bud_set_08 Bud_set_09 Bud_set_10   3 Leaf_drop_08 Leaf_drop_09 Leaf_drop_10   3   Post.bud_set._09 Post.bud_set._10   2     Yellowing_100%_10   1 Biomass   Height_09 Height_10 Height_11 3     Growth_period_10   1   Height_growth_cessation_09     1 Ecophysiology   Chsummer_09   Chsummer_11 2   Nmass_09 Nmass_10   2     Total tests: 18       Table S8. C List of F-values and p-values from ANOVAs comparing genotypes homozygous for introgressed P. balsamifera alleles, heterozygotes and homozygous for P. trichocarpa alleles in the first 880kb of chromosome 15.   Trait type Trait Fvalue p-value Phenology Bud_set_08 3.974 0.021 Bud_set_09 1.554 0.215 Bud_set_10 1.644 0.197 Leaf_drop_08 4.747 0.0101 Leaf_drop_09 1.719 0.183 Leaf_drop_10 3.542 0.0316 Post.bud_set._09 0.317 0.729 Post.bud_set._10 0.34 0.712 Yellowing_100%_10 0.707 0.495 Biomass Height_09 5.053 0.0076 Height_10 0.787 0.457 Height_11 1.098 0.336 Height_growth_cessation_09 2.022 0.136 Growth_period_10 0.608 0.546 Ecophysiology Chsummer_09 7.999 0.000609* Chsummer_11 9.242 0.000347* Nmass_09 6.225 0.00259* Nmass_10 2.983 0.0585  *significant differences after p-values were adjusted with Bonferroni correction (<0.0028)   Supporting information: Materials and Methods  Data sets used in this study including those generated here as well as those already published or in preparation for publication are presented in Table 1.  Table A1. List of the data sets used in this study, including those generated here as well as those already published or in preparation for publication. Data generated by this study is highlighted in orange (i.e. SNPs for local ancestry analysis, RASPberry; and gene sequence anaysis. See M&M and Supplementary Figure 2). Data previously published is highlighted in blue (i.e. phenotypic data, McKown et at. 2014) and in preparation for publication is highlighted in purple (RNA-seq, O. Corea, S. Biswas et al., preparation; PCA and preliminary RASPberry analysis, Geraldes et al in preparation). Data has now been archived in SRA and dryad. Data set Details Individuals  Usage Repository Whole genome data set (971k_SNPs)* Geraldes et al., in preparation 435 P. trichocarpa,   448 P. balsamifera PCA analysis (Appendix S1, SI; Geraldes et al., In preparation) to select reference and admixed individuals (25 pure P. balsamifera, 25 pure P. trichocarpa, 68 admixed)  In preparation Whole genome data set (from 971k_SNPs)*   25 pure P. balsamifera,            25 pure P. trichocarpa,            68 admixed Preliminary analysis in RASPberry to select the model with the highest log likelihood value †Dryad, ~SRA Whole genome data set (from 971k_SNPs)*   68 admixed Individual ancestries used in the input files for RASPberry analysis (ANCESTRY)  †Dryad, ~SRA SNPs chromosome 6, 12, 15 Suarez et al (this MS) 25 pure P. balsamifera, 25 pure P. trichocarpa, 68 admixed Local ancestry analysis(RASPberry). For the pure individuals only, Tajima's D, nucleotide diversity (π) (vcftools) and LD (Haploview, R) - in chromosome 15 - were estimated  †Dryad, ~SRA SNPs chromosome 15 Suarez et al (this MS) 435 P. trichocarpa Used to identify admixed individuals from northern populations (161) using NJ analysis (Mega). Also used to estimate LD (Haploview, R) - in 36 admixed individuals  †Dryad, ~SRA Gene sequence analysis (COMT1, COMT2) Suarez et al (this MS) 301 P. trichocarpa,   242 P. balsamifera FST value per SNP (Arlequin), haplotype distribution  †Dryad, ~SRA Gene sequence analysis (TTG1 ) Suarez et al (this MS) 297 P. trichocarpa FST value per SNP (Arlequin), haplotype distribution  †Dryad, ~SRA Gene sequence analysis (PRR5) Suarez et al (this MS) 302 P. trichocarpa FST value per SNP (Arlequin), haplotype distribution  †Dryad, ~SRA   RNA-seq data Corea et al., preparation 385 RNA samples from developing xylem in 197 accessions  (most in at least duplicate), and 389 RNA samples isolated from expanding leaves of defined developmental stage in 191 accessions (most in at least duplicate) We mined a population-wide RNA-seq dataset  grown at Totem Field (O. Corea, S. Biswas et al., preparation). Levels of gene expression (measured by FPKM values) were compared among the three genotypic categories (bb, bt and tt). ¶SRA Phenotypic data † McKown et at. 2014       ~SRA: Accession: PRJNA276056; ID: 276056 ¶SRA: Bioproject ID 300564 †Dryad: doi:10.5061/dryad.0817m  The input files and data used for the analyses implemented in this study have been archive in dryad: doi:10.5061/dryad.0817m (Table 2).  Table A2. List of the input files and data used for the analyses implemented in this study and now archive in dryad (doi:10.5061/dryad.0817m) Title Original SNP data ch6 12 15_replace Description SNPs in three chromosomes (6, 12, 15) for 50 reference individuals (25 pure P. balsamifera and 25 pure P. trichocarpa) and 68 admixed individuals Title 971Kb_filtered_dataset Description Filtered dataset(MAF >0.1, GR 0.95), for 50 pure and 68 admixed individuals. The initial dataset consisted of 971K SNPs (3691 genes, 19 chromosomes) Title alpha estimates in introgressed regions Description Data from Table 2. Alpha estimate for three introgressed P. balsamifera regions in P. trichocarpa, one in chromosome (Chr) 06 (region A) and two in chromosome 15 (B and C). Title Tajima and Nucleotide Diversity estimates Downloaded 1 time Description Data for Figure 2, Figure 4 Supporting Information (Tajimas' D) and Figure 7 Supporting Information (Nucleotide diversity). Title RASPberry Description Data for Figure 1, Figure 2 supportive information and Figure 3 supportive information. Title LD_Haploview Description Data for Figure 3 and Figure 6 supportive information. Title NJ analysis   Description Data from Figure 1 Supporting information and Figure 5 Supporting information Title Gene_sequences Description Data for Figure 4, Figure 8 supportive information and Figure 9 supportive information.  For local ancestry analysis in RASPberry, we selected 50 reference individuals (25 pure P. balsamifera and 25 pure P. trichocarpa) and 68 admixed individuals (36 P. trichocarpa individuals with P. balsamifera admixture, and 32 P. balsamifera individuals with P. trichocarpa admixture) from a collection of 435 P. trichocarpa and 448 P. balsamifera genotypes, using a previous genome wide admixture analysis and a PCA based on 971K SNPs from 3691 genes in all 19 chromosomes (Geraldes et al in preparation). This analysis also included other P. species (i.e. P. deltoides, P. fremontii, P. heterophylla, P. angustifolia).   Figure 1 shows eigenvector 1 (67.78%) separating P. balsamifera from P. trichocarpa and revealing admixed individuals, while eigenvector 10 (4.9%) separates P. trichocarpa samples along a north-south axis. Additional eigenvectors separated P. balsamifera and P. trichocarpa from other P. species (Geraldes et al in preparation). Based on eigenvector 1 values, we identified 25 pure P. trichocarpa (0.034 to 0.037), 25 pure P. balsamifera (-0.039 to -0.035), 36 admixed P. trichocarpa (0.019 to 0.029) and 32 admixed P. balsamifera (-0.031 to 0.006).    Figure 2 shows a detailed section of Figure 1 with P. trichocarpa admixed individuals selected for RASPberry analysis (orange), and those selected for LD decay estimates (black). The latter were selected within a set of admixed individuals with eigenvector 1 values raging from 0.024 0.029, to avoid pure P. trichocarpa and early generation hybrids.    Figure A1. Principal Component Analysis (PCA) plot of SNPs from P. trichocarpa and P. balsamifera accessions. The plot shows Eigenvector 1 vs Eigenvector 10 from a PCA based on 50 pure individuals (25 pure P. balsamifera and 25 pure P. trichocarpa) and 68 admixed individuals (32 admixed P. balsamifera and 36 admixed P. trichocarpa). SNPs from pure P. balsamifera (blue), pure P. trichocarpa (red) and P. trichocarpa admixed with P. balsamifera SNPs (yellow) were used in ancestry analaysis. This analysis is based on a previous genome wide admixture analysis based on 900K SNPs from 3691 genes in all 19 chromosomes (Geraldes et al in preparation).   109   109  1 2  3 Figure 2. Detail of the PCA plot in Figure 1 of SNPs from admixed P. trichocarpa accessions. Left: 4 Admixed P. trichocarpa accessions selected for RASPberry analysis (orange), and those selected for 5 LD decay estimates (black). 6  7  8  9  10  11 

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