4

Accepted Article Chhatre E. Vikram urn address Current dpieItorsinadMitnneo rseisHybrid Trispecies a of Maintenance and Introgression Adaptive 2 nttt fBhvoa eeis&Dprmn fEooyadEouinr ilg,Uiest of University Biology, Evolutionary and Ecology of Department & Genetics Behavioral of Institute This artic 10.1111/ mec.14820 doi: lead todifferences version between this andtheofPleasecite article Version Record. this as been and through typesetting, proofreading whichmay thecopyediting, process, pagination buthasThis article not review undergonefullpeer has for and accepted been publication Keywords: le isprotected rights by All copyright. reserved. ope nRneEg ouain of Populations Range-Edge in Complex 1 3 eateto ln ilg,Uiest fVrot ulntnV 05405 VT Burlington Vermont, of University Biology, Plant of Department eateto ilg,Ws ignaUiest,Mratw,W 25606 WV Morgantown, University, Virginia West Biology, of Department ymn NR iifraisCr,Uiest fWoig aai Y82071 WY Laramie Wyoming, of University Core, Bioinformatics INBRE Wyoming : ereg,amxue dpain yrdzto,seiscmlx poplar species-complex, hybridization, adaptation, admixture, rear-edge, cetdMnsrp MEC-18-0586-R1 Manuscript Accepted 1,4 ueM Evans M. Luke , ∗

uhrfrcrepnec ([email protected]) correspondence for Author ooao ole O80309 CO Boulder Colorado, 2 tpe .DiFazio P. Stephen ,

3 n tpe .Keller R. Stephen and , Populus ∗ 1 yrdzns seilya h agn fseisdistributions. in species adaptation of of margins edge the dynamics at range evolutionary especially in the zones, complex understanding hybrid hybrid for study multi-species implications Our a has in and dormancy. introgression populations, seasonal adaptive redox of of regulation of role in maintenance the involved transport, demonstrates metabolites ion wall metal cell regulation, and homeostasis, photoperiodic with associated from genes ancestry for excess represented 8% 23% and at 47% introgression balsamifera which of of patterns hybrids, non-neutral in of complex. loci evidence hybrid of found this we in well analysis, flow as clines gene early genomic recurrent including Using indicating overlap, a hybrids, range found backcross We of generation zone advanced species. the as three the throughout of present populations complex sympatric hybrid and tri-species allopatric 29 from individuals 296 in Using Canada. and States analyzed United we the (GBS), of genotyping-by-sequencing region of Mountain Rocky species the in three distributions between their of introgression margins the of at extent populations the in investigated genus process We the this of ranges. dynamics species the of about margins known is little widely species, in range introgression tree adaptive at distributed of adaptation understanding our facilitating improved have mechanism studies recent a Although into constitute limits. species may one another from of introgression background adaptive genomic environments, the marginal in occurring zones hybrid In Abstract 2 This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article CHHATRE Populus epciey eeotlg nlsssgetdteegnmcrgoswr enriched were regions genomic these suggested analysis ontology Gene respectively. , tal et sect. Tacamahaca ( .balsamifera P. ∼ 300snl uloieplmrhssgenotyped polymorphisms nucleotide single 83,000 , .angustifolia P. and , .angustifolia P. .trichocarpa P. tthe at ) and P. h ffc fhbiiainmyb anfidi ml,prpea ouain hr h ffcsof effects the where populations peripheral small, in magnified be Woolbright may 2011; hybridization Jump of & effect Hampe the “climate 2005; isolated Petit forms species & a (Hampe of edge populations rear relict” the where areas in refugial admixture shared glacial genomic into of as retreating evident periods taxa areas, historical related between example, contact For secondary ranges. promoted have species may of advance contraction the during occur also may (Petit expansions refugia glacial range Mediterranean northward of representing pathways out migration along prominent (Excoffier is admixture change trees, climate during shifts range with by habitats new 2017). into (Rieseberg expansion tolerance permitting stress or and breadth species niche increasing parental physiolog- up either opening to species, unavailable parental niches between ical regions genomic of introgression drive to variance associations plant-microbe or (Lamit plant-herbivore for consequences community-level into translate can Whitney 2009; of source important an be may How- and (Rieseberg variance 2001). novelty genetic Willis evolutionary increased & display (Fishman also hybrids may of zones hybrid fecundity ever, and fitness reduced from species resulting of isolation dissolution (Currat including taxa species 2016), diverged weakly of Larson between genetics & differences the (Harrison understanding isolation for reproductive laboratories and natural divergence Hybrid as 2016). recognized Buerkle been & long Larson (Gompert have & fitness zones and Harrison variability 1985; genetic recombina- for Hewitt outcomes and & diverse (Barton admixture with genomes 2014), the parental divergent from between resulting diversity process of tion evolutionary dynamic a is Hybridization Introduction 1. This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article ln eoe emt eepcal oeato yrdzto Reeeg19;Sli Soltis & Soltis 1997; (Rieseberg hybridization of tolerant especially be to seem genomes Plant nwdl itiue ln pce uha oettes yrdznsaecmol associated commonly are zones hybrid trees, forest as such species plant distributed widely In tal et 01 Evans 2011; tal et 00 Suarez-Gonzalez 2010; tal et 02 Floate 2012; tal et 2003). tal et tal et tal et 03 Grivet 2003; tal et 06.Slcinmyas c nti increased this on act also may Selection 2016). 08) n h nraei ri variability trait in increase the and 2018b), tal et eeto rvnItorsinin Introgression Driven Selection 08 n h enocmn freproductive of reinforcement the and 2008) tal et 09.Freape mn European among example, For 2009). 07 Whitney 2007; tal et 06.Cnesl,hybridization Conversely, 2006). tal et tal et 00 Goulet 2010; 04.Further, 2014). Populus tal et andb hrceiigteeznswt eoewd oeua akr (Goulet be markers can molecular introgression genome-wide adaptive with and Suarez-Gonzalez zones selection these on characterizing insights by some gained but understood, poorly are zones (Hersch-Green only species where Colorado, in River Miguel San angustifolia the as such site (Floate a at elevation species of gradient local a along Floate vary 2004; proportions ancestry tri-species where Alberta, in between zone multiple between na- occurs and introgression species poplar exotic of of plantations populations between tive found been also has ancestry hybrid (Whitham Complex function and composition ecosystem for toward implications introgression unidirectional primarily shows Utah between in River zone hybrid well-studied A 2018a). 2016, between resistance disease of trogression and (Suarez-Gonzalez known Geraldes well forces less evolutionary are the and boundaries fitness, species and traits maintaining of architecture genetic sections the for and introgression species of quences the (Stettler of well-characterized interfertility are so genus heterosis, the abundant of their to due programs breeding in (DiFazio species interfertile between edges. range in variation genetic standing shapes hybridization how of examples few Meirmans have 1997; currently (Rieseberg populations of size demographic al the et to relative large be may flow gene This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article In h clgcl eei,adgnmcfcosudryn h ies ucmsin outcomes diverse the underlying factors genomic and genetic, ecological, The CHHATRE .trichocarpa P. 00.Hwvr h oeo yrdzto nmria ouain sntwl tde,adwe and studied, well not is populations marginal in hybridization of role the However, 2010). Populus tal et r ypti,btbdrcinlitorsinocr rmrl ewe h atrtwo latter the between primarily occurs introgression bidirectional but sympatric, are tal et .trichocarpa P. aual curn neseichbisaecmopaeweerne overlap ranges where commonplace are hybrids interspecific occurring naturally , 21)fudeiec o nrgeso ewe h itrspecies sister the between introgression for evidence found (2014) tal et tal et .deltoides P. 06.I te ae,hbismyol cu mn oeo h sympatric the of some among occur only may hybrids cases, other In 2016). nnrhr rts ouba hc a eutdi smercaatv in- adaptive asymmetric in resulted has which Columbia, British northern in 08) o xml,i uoe ouaingnmcaaye freplicate of analyses genomic population Europe, in example, For 2018b). tal et , .balsamifera P. and 2014). .balsamifera P. tal et Populus .balsamifera P. 01.Furthermore, 2011). tal et and , pce ihntesm ein uha h contact the as such region, same the within species nQee (Meirmans Quebec in 96 DiFazio 1996; .angustifolia P. .angustifolia P. and .trichocarpa P. Populus tal et tal et .fremontii P. .angustifolia P. and nteOda ie drainage River Oldman the in 06 Martinsen 2006; 01.Hwvr h conse- the However, 2011). tal et .fremontii P. yrd r otnl used routinely are hybrids tal et (Suarez-Gonzalez 08) o example, For 2018b). 00.I oecases, some In 2010). , .deltoides P. ihsubstantial with , Populus .balsamifera P. nteWeber the on tal et tal et and , hybrid 2001). 2017; tal et P. loarcppltoso l he pce n hi ypti yrdzn oadestefollowing the address to zone hybrid sympatric their questions: and species three all of populations allopatric Evans on 2014; selection dormancy local to with consistent related (Keller genome variation traits genetic the standing physiological in signatures and and corresponding phenological with photoperiod growth, of of and suite gradients timing a along for adaptation known local are strong range, temperature their of portions allopatric (Keller In populations refugial glacial from descended relicts climate trichocarpa P. balsamifera three P. between introgression adaptive for test and America, alternative in favorable alleles certain of introgression backgrounds. the genomic driving selection positive and whole, a Populus (Christe recombinant F1’s against of selection fertility indicate despite zones hybrids hybrid replicate these in experiments garden common introgression prevent to (Lexer enough selection by strong driven not was isolation that but species, between incompatibilities between zones hybrid This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted that regions to correspond species between introgression selective experiencing regions Do 4. genomic certain on selection by driven being ancestry hybrid of genotypes in introgression evidence Is there 3. Is populations? hybrid in introgression genome of level range-overlap? of the zone is their extensive in How species these 2. in structure population of patterns the are What 1. Article ee edsrb e tri-species new a describe we Here, aeudroepstv eeto nteprna species? parental the in selection positive undergone have regions? hybrids? generation advanced of yrdznsbtenrpoutv slto iiigitorsino eoi iest as diversity genomic of introgression limiting isolation reproductive between zones hybrid tal et ,ti eincnit fnmru sltdra deppltoslkl representing likely populations edge rear isolated numerous of consists region this ), , .trichocarpa P. 06.Hr euepplto eoi nlsso eoewd N aito in variation SNP genome-wide of analysis genomic population use we Here 2016). .alba P. tal et and and , 00 Lindtke 2010; .tremula P. tal et .angustifolia P. 01 02 Evans 2012; 2011, tal et Populus aesonsrn otzgtcioaindet genetic to due isolation post-zygotic strong shown have tal et 06.Ti ugssa vrl eso a xs in exist may tension overall an suggests This 2016). yrdzn nteRcyMutiso North of Mountains Rocky the in zone hybrid 04.Mroe,woegnm tde ae on based studies genome whole Moreover, 2014). o w fteeseis( species these of two For . eeto rvnItorsinin Introgression Driven Selection tal et Populus 04 Zhou 2014; tal et pce nsection in species 01 Geraldes 2011; tal et 04 McKown 2014; .balsamifera P. Tacamahaca Populus tal et 2014). tal et and : oial eotdfo h rao h ok onan otiigtepttv yrdzn,but zone, hybrid putative the containing Mountains Rocky the of area the from reported torically (UTAH). population single a into sites undifferentiated genetically and of (Evans structure genetic population and variation of Samples genotypes. hybrid exhibiting possible individuals for preference a balsamifera with P. selected phenotypically were of zone hybrid genomics putative population the the investigating study and overlap larger in a range adaptation of of local part zones are known samples any These from and separated hybridization. Quebec well Ontario, Saskatchewan, geographically in areas distribution from natural Manitoba, its For from collected species. for each populations included of nine were core of sites range the Allopatric Utah, from sympatric. sampled Arizona, were are from and ranges reference, sampled species were the where populations Alberta zone and hybrid Wyoming putative Eight its streams. of mountain core the from separated geographically while populations, range, region, relict this climate Within edge rear 1). numerous (Figure form Canada and USA the of Mountains between zones of hybrid populations 21 across individuals 242 and from cuttings stem dormant sampled We Sampling (a) Methods & Materials 2. complexes. species of evolution the understanding for and regions edges these range in of zones hybrid phylogeography of of importance terms the in broadly more and populations, marginal in variation This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted angustifolia P. Article edsusorrslswti h pcfi otx faatv nrgeso sasuc fadaptive of source a as introgression adaptive of context specific the within results our discuss We eas nlddsmlsfo lsl eae hr species, third related closely a from samples included also We CHHATRE .angustifolia P. .angustifolia P. lk ris(u ie efsae,adtu ontrpeetarno apeo all of sample random a represent not do thus and shape), leaf size, (bud traits -like tal et ihncranppltos eageae ape rmgorpial proximal geographically from samples aggregated we populations, certain within .balsamifera P. Tbe1.W sdrnemp n ebru eod oietf putative identify to records herbarium and maps range used We 1). (Table .balsamifera P. scmo u aciydsrbtdaogflopan frvr and rivers of floodplains along distributed patchily but common is Chte&Keller & (Chhatre and .angustifolia P. .angustifolia P. tal et tal et eefo rvossuyo microsatellite of study previous a from were , 05.Det h eaieyfwsamples few relatively the to Due 2015). npreparation in hr hi agsoelpi h Rocky the in overlap ranges their where .trichocarpa P. .balsamifera P. .balsamifera P. .Acrigy re within trees Accordingly, ). hc snthis- not is which , hsconsisted this , .balsamifera P. srpre to reported is ed eefitrdfrqaiy(efc ac oepce acd eune rsneo h restric- the of presence sequence, no barcode site, expected tion to match (perfect quality for filtered were reads Cornell the by USA). HiSeq performed NY were Illumina (Ithaca, Facility sequencing an Diversity Illumina on Genomic and reads) University Bio- preparation bp library a (100 GBS on sequenced 48-plex. distribution single-end to size then 2000 fragment was for library GBS QIAquick assessed Each the library using resulting analyzer. cleaned the primers, and sequencing kit, Illumina purification append PCR to kit, cycles purification 18 PCR QIAquick for the amplified using PCR purified quantitites, equimolar in pooled were fragments Elshire lowing endonuclease genomic restriction of ng the 100 with digesting by DNA prepared were libraries genomic Briefly, sequenced). previously were of individuals sequenced newly all for genotypes (Elshire (GBS) genotyping-by-sequencing used We Genotyping SNP & Sequencing Illumina (b) agarose DNA. weight 1% molecular on high run of and presence (Invitrogen) and assay purity USA). BR determine CA, to Qubit Valencia, gels (Qiagen, fluorometric Kits the Mini using Plant quantified 96 was DNeasy DNA using DNA genomic whole of isolation se- species. whole-genome three previous the a of populations on based species (Evans poplar Columbia, study related British quencing from and Washington introgression in known drainages no river with from chosen specifically allopatric were of populations) locations Sample to zone. was hybrid aim putative the Our 1). (Figure Nevada and and historical Utah, or Idaho, contemporary Montana, any of identify areas nearby in occur does This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article utnswr otdadgoni otoldevrnetadfehlae eeue for used were leaves fresh and environment controlled a in grown and rooted were Cuttings a eunedt a rcse ihteTse B ieie(Glaubitz Pipeline GBS Tassel the with processed was data sequence Raw .angustifolia P. N s,timdt egho 4b,adaindt the to aligned and bp, 64 of length a to trimmed ’s), tal et ept paetasneo hsseisi h meit egbrodof neighborhood immediate the in species this of absence apparent despite , 21) oteed frsligrsrcinfamns h eutn barcoded resulting The fragments. restriction resulting of ends the to (2011)) tal et 04.I oa,tecretsuycnitdo 9 niiul rm29 from individuals 296 of consisted study current the total, In 2014). EcoT22I .trichocarpa P. .balsamifera P. n iaig9 nqebroe dpes(fol- adapters barcoded unique 96 ligating and tal et eeto rvnItorsinin Introgression Driven Selection netyi u ape of samples our in ancestry 01 nodrt banhg-est SNP high-density obtain to order in 2011) .trichocarpa P. and .trichocarpa P. .angustifolia P. N5 niiul rm8 from individuals (N=54 tal et eeec genome reference 04.Sequence 2014). ( .balsamifera P. .trichocarpa P. Populus elctsars 0fl rs-aiainieain.Brlt fcutrmmesi eevisualized were membership cluster at of Barplots iterations. cross-validation 10–fold across replicates of Inference ancestry genetic mixed ADMIXTURE in (Alexander for implemented clustering evidence genotype likelihood assess maximum To used we individuals, within 2015). the Jombart using & SNPs (Goudet 10,000 HIERFSTAT of library subset random a using populations all pairs over (4) pairwise estimated and also zone, We hybrid VCFtools. the using in populations among the (3) of species, populations within 29 populations in SNPs ( 83,835 differentiation Genetic all across species. structure three population of levels overall assessed We Events Migration & Admixture Structure, Population (c) performance high Moran 2012). (ARCC Mount Wyoming the of on University performed polymorphic the were were at computations that cluster All chromosomes computing 19 species. all one from least SNPs at 83,835 in obtained we species, ( three excess Wahlund all heterozygote from to with due sites heterozygotes removed of and deficit individually a performed we to bias, lead this could avoid To species effect. more Composite or under two equilibrium. be Hardy-Weinberg involving may from sets that deviations data for alleles SNPs rare all discarding tested avoid we to Finally, threshold selection. frequency allele minor minimal a set data missing genotype downstream for used and files (Danecek (VCF) VCFtools Format using Call filtering Variant to converted were data Details type removed. were variants for duplicate calling and genotype assembly SNP reference of the on based called were (SNPs) (Tuskan 3.0 version This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

AcceptedK Article efitrdSP oke nyballcsts ihidvda-iemsigdata missing individual-wise with sites, biallelic only keep to SNPs filtered We CHHATRE 24uigamdfidDSRC 23Pto cit(Raj script Python v2.3 DISTRUCT modified a using =2–4 tal et K < 0,gntp ult (GQ) quality genotype 20%, tal et a eemndbsdo h oeterrrt eeae sn 00bootstrap 2000 using generated rate error lowest the on based determined was 09.Frti nlss eeautdmdl from models evaluated we analysis, this For 2009). tal et 06 sn W L ubn20) igencetd polymorphisms nucleotide Single 2009). Durbin & (Li BWA using 2006) .trichocarpa P. tal et F ST 2011). χ a esrd()btenseis 2 mn allopatric among (2) species, between (1) measured was ) 2 eerpre rvosy(Evans previously reported were et fHryWibr iltoswti ahspecies each within violations Hardy-Weinberg of tests ≥ F 0 leedepth allele 90, ST Wi okra 94 ewe l population all between 1984) Cockerham & (Weir pairwise.WCfst < P ≥ ,adidl eoe.W i not did We removed. indels and 5, 0 . 0) fe obnn samples combining After 001). tal et K o5subpopulations. 5 to 1 = 04 har 08.To 2018). Chhatre 2014; tal et ucinfo h R the from function 04.SPgeno- SNP 2014). < 0,locus-wise 50%, eeautd1 needn rgn eoyi lse Tbe3 opiigprna,F,F and F2 F1, parental, comprising 3) populations. (Table allopatric classes between genotypic differences progeny fixed independent 12 divergence nearly evaluated frequency or We allele fixed of (e.g. level highest species the parental showing the SNPs between 2002). 375 Thompson the & to (Anderson analysis our NEWHYBRIDS restricted gener- using We advanced classes or genotypic (F1) backcross) early and produce (F2 zone hybrid ation this in populations that evidence evaluated We Hybridization Recurrent of Extent (d) was error 2012). residual Pritchard the until & flow events (Pickrell migration gene minimized of for number allowed total We the SNPs. increasing by contiguous populations 500 between due of windows non-independence for analyzing accounted by We disequilibrium linkage taxa. four to all of across subset available a were on that based (n=11,794) was SNPs analysis This https://phytozome.jgi.doe.gov). phylogeny. ( from Cottonwood available population Eastern - a related v2.1 distantly estimate WV94 more to the admixture with rooted with was drift 2012) tree phylogenetic genetic Pritchard The of & model (Pickrell Gaussian TREEMIX migration a used likely analyze we most to admixture, the generated and that populations these them of between (Suarez-Gonzalez history events millennia joint the for understand existed better have To may 2018a). retreat three and all advance of glacial limits during range geographic current (Levsen proximate species and relationships, phylogenetic close the with ancestor of common time divergence shallow a with genetic Hardy-Weinberg 10 to to up conditions for run tested same and the run (i.e. ADMIXTURE applied clusters original We the in SNPs. as 83,835 set original data the this of 11,794 of consisted ( dataset species additional 5 from those euphratica with samples analysis study ADMIXTURE the our repeated combining we by species, Populus other from introgression potential for test This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article w forsuyspecies, study our of Two , .tremula P. K subpopulations). tal et and , 02,teptnilframxueeet rsn rmscnaycontact secondary from arising events admixture for potential the 2012), .angustifolia P. .fremontii P. .trichocarpa P. ∼ 600yas(Levsen years 76,000 Hme aaadn20;Cervera 2004; Dayanandan & (Hamzeh .Det ieetdt ore,ti diinlspecies additional this sources, data different to Due ). and .balsamifera P. eeto rvnItorsinin Introgression Driven Selection tal et r eetyseitdsse taxa sister speciated recently are , 02,adsaeamr distant more a share and 2012), .deltoides P. tal et , 05.Given 2005). .nigra P. Populus .deltoides P. tal et 2016, , P. eta xettosa ahlcswr eodda h eaiegntpccnrbto fec fthe of each of contribution genotypic relative the as from recorded Deviations were a locus locus. each under each at for expectations proportions simulations neutral parametric genotype 1,000 expected on the based model, to demographic ancestry neutral locus-specific of clines genomic observed when analyses clustering membership cluster genotypic used to We in analogous ancestry, species. 7,523 interspecific between of of higher index hybrid or subset a 0.8 estimate of a to INTROGRESS difference analyzed frequency we allele absolute Therefore, an showed that species. SNPs parental between large differential a show frequency that regions allele genomic analyzing requires introgression of inference Informative between samples. introgression is on INTROGRESS analysis in this implemented focused 1), (parent model we the species, parental Because two 2010). to limited Buerkle & INTROGRESS based (Gompert likelihood R maximum in the package using genotypes hybrid over-representation in in results ancestry introgression locus-specific genomic of which local & to (Wolf of extent isolation the loss reproductive studied We in in involved 2017). result are Ellegren or that divergence”) regions of islands other adaptive “genomic of (i.e., an introgression adaptation provide preventing that regions while genomic hybrids, of in introgression advantage the favor may zones hybrid in Selection Introgression Differential & Selection (e) 100,000 first the discarded we which of sweeps, 200,000 burn-in. of as total sweeps a for space for parameter prior MCMC Jeffrey’s the and numbers seed unique using BRIDS For hybrids. angustifolia all putative excluded as we designated analysis, were second populations sympatric the the and species, and parental poplars two balsam the the of populations Allopatric group. poplar” analy- separate two combined performed we we First, NEWHYBRIDS, estimate ses. in to species means 2 straightforward than more a among not classes is genotypic there Because hybrids. backcross generation advanced This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article CHHATRE .balsamifera P. n h yrd.Frec aast estu he needn uso NEWHY- of runs independent three up set we set, data each For hybrids. the and tal et .balsamifera P. prn )adtepttv yrd poey,adomitted and (progeny), hybrids putative the and 2) (parent .trichocarpa P. and K .Tehbi ne a hnue ocmaethe compare to used then was index hybrid The 2. = .trichocarpa P. ape,rtiigonly retaining samples, niiul oehrit ige“balsam single a into together individuals Pi and .angustifolia P. Theta aaees n explored and parameters, .balsamifera P. eecasfidas classified were .angustifolia P. .trichocarpa P. and P. 000sep eedsadda uni n aawr olce o h et5,0 wes We sweeps. 50,000 next the initial for An collected sweeps. were 5,000 data of and length burn-in a as with discarded each were runs sweeps pilot 50,000 20 using optimized were conditions Run in adaptation within Local adaptation tions). local of evidence for tested and also observed the We with overlap loci. random 1000 SNP the using re-calculating INTROGRESS tested then was and windows, sweeps sweep selective overlap the under of of permutations Significance regions genomic outliers. CLR introgression and with to outliers regions comparisons introgression retained for between species and each 100kb, within of 1% regions top chromosomal the in in CLR the computed We Nielsen of 2013). test parental (CLR) pure ratio the likelihood within ite sweeps Selective populations. of parental regions populations the and outliers in introgression selection between positive overlap for under tested we hybrids, in introgression ferential this INTROGRESS iterations. an repeated 100 had We all that in loci 0 populations. those = as parental outliers of robust identified the set and on times original based 100 the clines procedure plus genomic re-estimated populations and hybrid populations 7 hybrid 8 remaining the possibility, of this against 1 guard dropped primarily To randomly is zone. we analysis hybrid our the within in populations positives among false structure for genetic potential from last the the Thus within Results). occurred has (see that generations hybridization several of consists mostly and diverse The genetically is 2011). sampled 2009, the is Buerkle among zone & positives hybrid (Gompert false introgression the adaptive for for and/or potential loci the large, outlier to is leading admixture populations, since structured multiple time of small, composed very is population admixed the if interpretation. further of purposes the for outliers as (0 considered p-values not intermediate were significant at with expectations SNPs neutral introgression. violating differential SNPs of interpreted evidence We hybrids. the to species parent two This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article oass fslcinwti h aetlseiscnrbtdt eoi ein xeinigdif- experiencing regions genomic to contributed species parental the within selection if assess To effects demographic neutral to sensitive be may INTROGRESS behind model parametric The .trichocarpa P. .angustifolia P. ( .angustifolia P. .balsamifera P. , .balsamifera P. a o nldddet ml apesz ihnms popula- most within size sample small to due included not was tal et a etduigBYSA Fl agot 2008). Gaggiotti & (Foll BAYESCAN using tested was and , 20) sipeetdi we (Pavlidis SweeD in implemented as (2005), eeto rvnItorsinin Introgression Driven Selection .trichocarpa P. eetse sn h compos- the using tested were Populus yrdzn we zone hybrid .balsamifera P. < P > Populus P P 0 = as 0 = -value tal et . 05) au rmteercmn eti N2O evsaie h eue EIOcutr using clusters REVIGO matrix. reduced similarity semantic the pairwise visualized FDR-corrected the We highest of SNP2GO. scaling the in multi-dimensional with test term enrichment the the keeping from on value based cluster each of resentative REVIGO ( using similarity summarized semantic was of terms GO enriched of redundancy (Supek using Functional determined enrichment 0.1. of of significance q-value SNPs the a and re-sampling expectations, randomly and null by upstream determine generated Mb to was times 1 enrichment 100,000 of term window GO a SNP. within each genes candidate from with compared downstream associated we density, terms GO marker for modest SNPs relatively non-candidate our and hybrids generation early preponderance in showing (c) in loci among of deviation subsets significant of two showed (d) also and that classes, loci genotypic outlier expected (b) the 100 of the subset on the based (c) outliers introgression datasets, (b) resampled populations, hybrid N=8 all with run (Szkiba INTROGRESS SNP2GO gle package R the using assessed was al SNPs et outlier with terms GO of enrichment for the ontol- on gene based using terms INTROGRESS (GO) from ogy outliers introgression of enrichment functional for tested We Enrichment Functional (f) Evans (see variables details). climate additional multivariate the of using components 2013) principal Coop (G¨unther BAYENV second & from and results first on (Evans based was species adaptation that local in of selection analysis be local to for 10,000 scans in genome tested locus reported similarly 1 We of 2014). with Whitlock associated expectation & regions prior introgressed (Lotterhos rigorous for positives false a minimize set to We selection local adaptation. under effect local locus-specific of the history from a selection of positive of strength the inferred This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted angustifolia P. Article 04.W eetdti nlssfrdffrn eso oi a nrgeso ulesfo sin- a from outliers introgression (a) loci: of sets different for analysis this repeated We 2014). CHHATRE tal et 01.W sdRVG ocutrcoeyrltdG em ae nterdegree their on based terms GO related closely cluster to REVIGO used We 2011). tal et lee ntehbis ie h ag xetddge flnaedisequilibrium linkage of degree expected large the Given hybrids. the in alleles > 0 ae nteSme iiaiymaue,adrtie em rep- terms retained and measure), similarity SimRel the on based 70% .trichocarpa P. .trichocarpa P. eeec eoeantto 30 ttsia support Statistical v3.0. annotation genome reference oiudrlclaatto sn previously using adaptation local under loci tal et 04.The 2014). α with , > α tal et .trichocarpa P. indicative 1 21)for (2014) vs − log10P deficit vs nlsswt h v ugopseisddntrva infiatamxuefo n fte into them of any from admixture significant reveal not did species outgroup five the with analysis at observed admixture specific At within overlap. revealed range was of substructure regions population the additional in from hybrids ancestry tri-species contained of also presence JKH, populations the (CYH, indicating these Wyoming in and individuals Alberta of Some Mountains MSG). Rocky SSR, the in species these between evident ture where RMPANG) RMP, Utah At JKH, in WYSR). SSR, populations CYH, some (MSG, as Alberta well and as Wyoming, Colorado, in populations at structure for population of division major The between 2a). was (Figure contact secondary of region the of of populations allopatric the within ture between differentiation ( interspecific the populations among differentiation genetic (Keller zone, estimates hybrid previous with line in and divergence, ( lower substantially was poplars balsam trichocarpa as angustifolia low as P. from ranged SNPs 10,000 chosen randomly (MMT of subset a on based divergence either for lations differentiation (Evans genetic strong revealed of zone hybrid populations the among of outside structure population of Analysis Admixture & Structure Population of Patterns (a) Results 3. This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article netyaayi sn eoyi lseigat clustering genotypic using analysis Ancestry vs tal et F)t .5 (AZPW 0.754 to OFR) seSplmnayTbe1.A xetd h endffrnito ewe h two the between differentiation mean the expected, As 1). Table Supplementary (see K .angustifolia P. 05,weestebla olr hwdltl eei ieetainaogpopu- among differentiation genetic little showed poplars balsam the whereas 2015), =3, n h asmppas n oe ieetainbetween differentiation lower and poplars, balsam the and .balsamifera P. .trichocarpa P. .angustifolia P. n h w pce fbla olr,wt ditr lal evident clearly admixture with poplars, balsam of species two the and K ( eaae from separated F vs 2and =2 ST KKMS) ihtelretpiws ieecsbetween differences pairwise largest the with SKYKOMISH), 006 or =0.046) ( .angustifolia P. F F .balsamifera P. ST ST K 007,cnitn ihtermr eetevolutionary recent more their with consistent =0.037), 013,cnrigpeiu nig nti species this in findings previous confirming =0.153), .angustifolia P. 3rmie nhne.Cmie ADMIXTURE Combined unchanged. remained =3 .balsamifera P. .trichocarpa P. K eeto rvnItorsinin Introgression Driven Selection 2sbouain hwdltl on admix- no to little showed subpopulations =2 and , tal et .trichocarpa P. .angustifolia P. F ST .balsamifera P. steol pce rsn UA & (UTAH present species only the is 001 a iia nmgiueto magnitude in similar was =0.091) 01 Evans 2011; Fgr b,wt usata admix- substantial with 2b), (Figure ( F ST 008.Piws population Pairwise =0.028). and u h atr finter- of pattern the but , sawoe( whole a as tal et .angustifolia P. .balsamifera P. 04.Wti the Within 2014). K 4(iue2c), (Figure =4 .angustifolia P. Populus F F ST ST =0.094). =0.0021 outside and K =2 P. , fmgain eeflwbtentebla olr a vdn rmapplto neta to ancestral population a from levels evident higher was these At poplars balsam trichocarpa S3). the (Figure P. variance between residual flow the gene reduced migration, and of fit model improved 10 the to outside 7 from RMPANG into allopatric flow involving gene zone for evidence hybrid also was There admixture. to contributing population WYSR Wyoming the into poplars of balsam two the of ancestor common the into from ABOR detected of from ancestor also JKH, intermediate into was an RMPANG from but from and RMPANG), MSG, (e.g. and zone hybrid (RMP the Colorado throughout elsewhere in extensive populations flow sympatric gene the bidirectional between extensive strongest showing pattern of migration across populations events prominent migration between most 7 the estimated an with in tree, resulted populations the between flow gene of for group Allowing main the 3). to prior or (JKH) to split positions species basal of occupied clusters also population JKH) main and SSR, the (MSG, clustering genotypic in admixture specific angustifolia S3). P. Figure in & relationships phylogenetic 3 established (Figure confirmed flow section TREEMIX gene by divergence extensive estimated of tree by pattern population accompanied complex The species a parental revealed three populations the sampled among the of history demographic The Flow Gene & Divergence Historical (b) species. outgroup the ( species study Further three the S5). of two (Figure within sample study original our from separate at At lowest separately. the clustered was species error validation Cross populations. study our This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted angustifolia P. Article CHHATRE Tacamahaca noteWoigpplto S of SSR population Wyoming the into rmtetobla olr Fgr ) ouain hwn ihlvl finter- of levels high showing Populations 3). (Figure poplars balsam two the from tal et osbyidctn h itrcpeec fa neta asmppa eepool gene poplar balsam ancestral an of presence historic the indicating possibly ihagetrpooto ftettlgntcditsprtn ouain of populations separating drift genetic total the of proportion greater a with , .balsamifera P. K .balsamifera P. .balsamifera P. 4tefieotru pce omdasnl ooeoscluster homogenous single a formed species outgroup five the =4 .balsamifera P. and .angustifolia P. .angustifolia P. nraigtenme fmgainrue from routes migration of number the Increasing . and .balsamifera P. and .trichocarpa P. .balsamifera P. .angustifolia P. eeflwbtenteeseiswas species these between flow Gene . ouain noCH.Gn o was flow Gene CYH). into populations K K ouain MG S)(Figure SSR) (MSG, populations lseigrvae substructure revealed clustering 3weeortremi study main three our where =3 iegn ihrpirt the to prior either diverging , Fgr c&d;apattern a d); & 3c (Figure ,btn nrgeso from introgression no but ), ne-pcfi eoyi lse Tbe3.O hs,152sts(3)soe more showed (43%) sites 1,592 these, the of Of one 3). least (Table at classes for genotypic frequencies neutral inter-specific from deviation significant showed 3,263 ( SNPs, model significant demographic neutral a under frequencies genotype expected from deviation significant showed INTROGRESS by estimated clines Genomic Introgression Driven Selection (d) multiple uncovered reflecting we 8) of the addition, out towards individuals (7 backcrosses In individuals F1 of majority of the detected. with consisted (N=8), also hybrids backcross analyses were generation advanced admixture individuals F2 in three 0.5 although near (N=21), values ancestry with individuals of between backcrosses generation without and with thus (both and poplars genome reference the from divergent was calling. hybrid variant a during in properly map alleles to two failed the could of hybrids in one deficit if heterozygote polymorphisms arise although ancestral also species, shared each reflect of 1) populations probably or pure 0 These within near segregating values. index expected (hybrid types the parental above while slightly index, were hybrid relative their heterozygosity from interspecific expectations of levels maximal reduced to slightly show in- to tended of individuals indicative Hybrid towards backcrossing 1, 4). hybrids to generation 0.5 advanced from and continuously F2) (F1, somewhat termediate ranging index hybrid with identified were rang- ( ADMIXTURE, 0 from to proportions close from ancestry ing to correspondence close showed index hybrid The Hybridization Introgressive of Extent (c) overlap. range previous from event during flow hybridization gene historical a Finally, of 2). populations (Figure Arizona analysis the ADMIXTURE the from evident also was that This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article sineto niiul nohbi eoyecassbetween classes genotype hybrid into individuals of Assignment .angustifolia P. .balsamifera P. .angustifolia P. .trichocarpa P. .angustifolia P. lk)t prahn ( 1 approaching to -like) parent. into hwdeiec o 1 2 n eea advanced several and F2, F1, for evidence showed ) P n h asmppas(al ) h majority The 2). (Table poplars balsam the and .deltoides P. 0 o ,2 fte753SP.O h 3,723 the Of SNPs. 7,523 the of 3,723 for =0) eeto rvnItorsinin Introgression Driven Selection .balsamifera P. a paet oetal reflecting potentially apparent, was .angustifolia P. lk) ubro hybrids of number A -like). .balsamifera P. n h balsam the and .angustifolia P. Populus (Figure eetv we noeo h he aetlseis(iueS) ie eoewd ubrof number genome-wide a Given a S6). of (Figure evidence species showed parental that three windows) the (N=120 of one regions in genomic sweep of selective 1% upper the with overlapped species. the between admixture and divergence of process neutral the reflects a on adaptive are that ancestry markedly was loci candidate F of distribution the however, lower towards loci; shifted candidate and neutral of set bined per-locus found we prediction, regions this for genomic with Consistent than species introgression. between resisting divergence or less neutrally show acting and zone hybrid the within mogenized of background nomic the of SNPs (12%) 213 and (17%) 308 in observed respectively. were total deficit and excess heterozygote specific more fell showed outliers more (8%) These showed 138 (47%) while 3). expected, 832 (Table deviated runs categories: also 100 major 1,016 all outliers, three across 1,764 into classes these significant genotypic were Of expected that their 6a). tested in (Figure 7,523 significantly runs of replicate out INTROGRESS outliers 100 SNP all 1,764 in of set a identified populations vidual regions genomic of frequency high S4). the (Figure was populations multiple note across particular Of hybrid S4). given showing Figure a for & background 5 genomic the (Figure from index deviated that evident ancestry were inter-specific introgression of differential regions experiencing as regions Genomic respectively). proportions 33%, similar in and occurred (28% deficit and excess heterozygous interspecific more expected; showed than (25%) ancestry 949 whereas expected, than ancestry homozygous This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. AcceptedST Article .angustifolia P. fte174itorsinotir htwr infiati l 0 eapigieain,51 iterations, resampling 100 all in significant were that outliers introgression 1,764 the Of fslcini neddiigaymti nrgeso of introgression asymmetric driving indeed is selection If indi- of exclusion to outliers introgression of robustness the assess to analysis resampling The mn ule oii ossetwt eeto nrgesn eoi ein of regions genomic introgressing selection with consistent is loci outlier among CHHATRE .angustifolia P. tal et drvdallsi h yidzn ob agn rm001t .7 o h com- the for 0.777 to 0.021 from ranging be to zone hybird the in alleles -derived F .balsamifera P. ST netyi yrd akrse to backcrossed hybrids in ancestry auscmae opttvl eta oi(iue6) hsrdcinin reduction This 6b). (Figure loci neutral putatively to compared values .balsamifera P. hnw hudepc hs eoi ein obcm ho- become to regions genomic these expect should we then , .balsamifera P. eoi akrud hl h eto h genome the of rest the while background, genomic ooyosacsr hnepce.Inter- expected. than ancestry homozygous .angustifolia P. .balsamifera P. .angustifolia P. .balsamifera P. ooyosacsr than ancestry homozygous seilyoe evident ones especially , netyit h ge- the into ancestry .angustifolia P. homozygous F ST 2) ncnrs,nn eeerce o hs hwn oe rprinof proportion lower a of showing those proportion S2b for higher Tables enriched a 7; were (Figure none binding contrast, ion In metal S2c). through excess & homeostasis with redox loci cell of for maintenance enriched including were genotypic terms of proportion GO expected 11 from resampled among deviation classes, significant However, 100 showing all outliers regulation). 1,764 across photoperiodic the significant of (GO:0009416, subset term loci the enriched 1,764 single the a Among was there maintenance 7). runs, and (Figure metabolism), homeostasis xyloglucan redox and as cell glucan such of apoplast, components wall (i.e. cell glucan of cellular terms and metabolism GO cellulose and enriched Other biosynthesis involved S2). other Table redundancy 7; and (Figure minimal metals membranes with of cell across scores transport Al) similarity and and on Mg, binding Fe, based including (Zn, terms cations groups, GO redundant of minimally Clustering 52 S2a). in (Table resulted terms (GO) ontology gene 91 for between introgression angustifolia differential P. showed that SNPs flanking regions Genomic Outliers Introgression of Enrichment Functional (e) study. our from SNPs 78 in study among genomics Similarly, population (Evans broader zone. a hybrid in adaptation the local in showing introgression regions genomic differential with associated were evidence loci was these there while finding, among this adaptation with Consistent local between of overlap S7). observed (Figure the significant that not indicated was expected tests outliers is permutation the what accordance, to In close chance. is overlap by observed occur the to Thus, loci. fall among to equilibrium linkage SNPs and outlier species of number 1764 the be to expect windows would 120 we within species, 3 in tested (N=3,946) windows 100kb This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article tal et 04 BYN C/C) oesoe vra ihte174itorsinoutlier introgression 1,764 the with overlap showed none PC1/PC2), (BAYENV 2014) o h NRGESrnwt l yrdppltoswr infiatyenriched significantly were populations hybrid 8 all with run INTROGRESS the for .balsamifera P. .balsamifera P. × 3946 120 netista expected. than ancestries 4 suigidpnec fbnfiilmttosamong mutations beneficial of independence assuming 54, = loarcppltosfr1 Ns(FDR SNPs 10 for populations allopatric eeto rvnItorsinin Introgression Driven Selection .angustifolia P. nety(3 outliers), (832 ancestry .balsamifera P. .angustifolia P. < .trichocarpa P. Populus .) oeof none 0.1), and or efudta eurn neseicgn o hrceie h eoi iest fisolated of diversity genomic the ulus characterizes flow gene interspecific recurrent that found We Range-Edge in Flow Gene Recurrent (a) hybridization potential. that adaptive unique role and the the structure of and genetic light their populations, in in edge results plays range these in discuss We occurring 1997). processes (Rieseberg genetic found range population conditions species environmental of a novel source of or edges a stressful the as near to hybridization adaptation of for importance variation the genetic reflect segregating signatures may These populations for range-edge zone. evidence in hybrid the selection genome-wide in of extensive genomes was parental There the between introgression backcrosses. selection-driven early generation both advanced including and ancestry, inter-specific F2) of (F1, patterns complex with hybrids contained overlap of of edge range northern poplars, the balsam two near the and of edges range eastern and southern the limits. range their at overlap between introgression adaptive of assessment genome-wide balsamifera P. al et documented well is hybridization genus While the flow. gene in directional repeated via local extinction driving to or pools genomes gene divergent between variants adaptive transferring consequences for stressful evolutionary has occupy the hybridization and that amplifying abundances potentially lower limits, at physiological occur their typically near ranges environments species Pop- of boundaries. edges species the of near maintenance the ulations or ranges habitats distributional peripheral their to of adaptation edges to the contribute at may species between flow gene how examined have studies Few Discussion 4. This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article u eut dnie r-pce ope of complex tri-species a identified results Our ouain rwn ntezn foelpbtenterneegsof edges range the between overlap of zone the in growing populations 21),adrcn eot aehglgtdteiprac faatv nrgeso between introgression adaptive of importance the highlighted have reports recent and (2014)), CHHATRE Populus and tal et .trichocarpa P. nNrhAeia(..Eknadr(94;Talbot (1984); Eckenwalder (e.g. America North in (Suarez-Gonzalez .angustifolia P. Populus Populus ouain rmti eeial ies zone diverse genetically this from Populations . tal et 06 08) u td rvdstefirst the provides study our 2018a), 2016, nteNrhr ok onan,along Mountains, Rocky Northern the in Populus yrdZones Hybrid .balsamifera P. pce pcfial hr they where specifically species tal et and .balsamifera P. 21) Geraldes (2012); .trichocarpa P. Pop- , P. , vnsapa ob rqetadbdrcinlbetween bidirectional and Migration frequent be species. three to these of appear history events the in recurrent been have may edges range at hybridization hybrids. of generation zones advanced of in formation occur the can and species progeny viable three to all leads involving and sampled introgression contact we secondary origin, that recent individuals relatively hybrid of most be although may that species. suggest parental the results of current genomes our the between Nevertheless, asymmetrically varies viability hybrid if determine to al et cotton- narrowleaf the with balsamifera only observed been have (Keim backcrosses wood the where Utah in the zone in hybrid known is introgression asymmetric Such genomes. parental balsamifera predominantly with to backcrossing repeated indicating present introgression of overlap. zone ranges unique their a of be edges to the appears where Mountains lineages (Fig. 3 Rocky species these the related among in other 5 zone from hybrid introgression this of other Thus evidence from no S5). found contributions we ancestry sample, our to of due outside result spp. also could patterns admixture complex of populations other tween of reminiscent tri-hybrids, be to appeared tween between hybrids contained F1 populations frequent showed balsamifera Most population P. RMP 2). the (Figure example for overlap species, range two of between hybrids zone the mixed within of range populations a in with individuals ancestry reveals and allopatric, are populations where demes pure relatively trichocarpa This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article h vltoayhsoyo ouainsltigadmxn ute ugssta interspecific that suggests further mixing and splitting population of history evolutionary The also were hybrids generation advanced of range a F2’s, or F1’s be to appear hybrids many While 08) uuesmln hudtre rae ag fidvdaswti hshbi zone hybrid this within individuals of range broader a target should sampling Future 2018a). .balsamifera P. and , lk ris u ecno ueotaba ntedrcino yrdcmaiiiybetween compatibility hybrid of direction the in bias a out rule cannot we but traits, -like yrdzns nwihitorsini isdtowards biased is introgression which in zones, hybrid tal et and .angustifolia P. 99 Whitham 1989; .angustifolia P. .balsamifera P. .balsamifera P. and .trichocarpa P. eoyi lseigcerysprtsec fteeseisinto species these of each separates clearly clustering Genotypic . hl h S ouainsoe yrdzto xlsvl be- exclusively hybridization showed population SSR the while , tal et netylkl eet u apigo niiul ihmore with individuals of sampling our reflects likely ancestry , .angustifolia P. 06,adi lorpre between reported also is and 2006), neetnl,svrlidvdasi te populations other in individuals several Interestingly, . .balsamifera P. Populus eeto rvnItorsinin Introgression Driven Selection and , .balsamifera P. yrdznsweetihbiseitbe- exist tri-hybrids where zones hybrid .deltoides P. h rvlneo akrs hybrids backcross of prevalence The . .balsamifera P. .angustifolia P. (Floate and .angustifolia P. .trichocarpa P. tal et (Suarez-Gonzalez and 06.While 2016). Populus .fremontii P. Populus and nthis in P. ehd(opr url 09 a esniiet ffcso eei rf.Freape if example, hybrid For the where drift. species genetic the of of representative effects not to are sensitive frequencies be population (parental) can reference INTROGRESS 2009) the Buerkle that given & selection (Gompert of evidence method as analysis clines genomic during expectations Torre La De (52%; Lexer spruce (35%; in as such loci, neutral zones Hamilton to hybrid 76%; candidate in (2014); of introgression ratio of high studies a Other found index). also on have hybrid based (i.e., expectations admixture that demographic of SNPs) neutral degree tested beyond overall of hybrids the (23% in genome ancestry the excess Genomic of of portion patterns zones. large showed a hybrid revealed in resampling selection with analysis hitchhiking clines for potential enhanced creating disequilibrium, 4). (Figure consistent regions introgressed no among showed heterozygosity analysis interspecific clines of genomic deficit and or were excess populations, hybrids zone generation hybrid advanced and in F2 common recombinants. relatively found we against study, acting our selection In of hybrids. generation evidence advanced little of lack apparent an and progeny the in hybrids dilution alba or incompatibilities intrinsic Christe to adaptation. due between hybrids local flow recombinant of gene of recurrent fitness of in face reduction the a in is integrity species species maintaining for mechanisms the of One Hybrid in Introgression Driven Selection (b) refugia). glacial into in species contact of secondary previous expansion during range occurring many and (i.e., distributions divergence happened current the that their events pre-dating hybridization even of potentially vestiges ago, contain generations probably Mountains Rocky the in balsamifera hybridization P. of allopatric history current involving longer-term events a migration of of for populations inference the evidence from Additional comes species two S3). these between Figure & 3 (Figure region This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article neseichbiiainbtendvretlnae a raelrebok flc nlinkage in loci of blocks large create can lineages divergent between hybridization Interspecific nErp hwdslcinaantrcmiathbis edn ooerpeetto fF1 of overrepresentation to leading hybrids, recombinant against selection showed Europe in CHHATRE tal et .angustifolia P. and tal et 21).I spuett ecuiu bu nepeigdvain rmneutral from deviations interpreting about cautious be to prudent is It (2010)). .trichocarpa P. tal et tal et 21),huemc 9% Teeter (91%; mice house (2013)), nWoig(YR n h omnacso fcontemporary of ancestor common the and (WYSR) Wyoming in 21)dcmne hthbi oe between zones hybrid that documented (2016) ouain.Tu,hbi eoe nteae fsympatry of area the in genomes hybrid Thus, populations. Populus tal et Genomes 21),adErpa poplars European and (2010)), .tremula P. and tal et P. eoi ein novdi omny n osblt sta die ouain of populations admixed that is possibility one dormancy, in involved regions genomic between introgression including in roles endodormancy physiological seasonal diverse of Rinne plays release example and For walls, cell cycling. plant dormancy in affects deposited which matrix metabolism glucan cellular as the well as for regulation enrichment term photoperiodic GO involved study, outliers present the introgression In elevation. and temperature photoperiod, to responses Keller genes, of time populations flowering edge of study range-wide (Olson recent photoperiod a of In length to tied closely is gradients driven latitude to (Soolanayakanahally phenology and climate growth of in adaptation local substantial introgression. shows and differential range of signal the underlie may (Figure homeostasis redox cell of maintenance and membranes 7). across transport ion functions metal metabolic as and such regulation photoperiodic with for associated overrepresented significantly terms were ontology SNPs Gene these environments. a range-edge provides that suboptimal introgression in through advantage variation selective genetic adaptive capture to opportunity an present from often most genomes, parental balsamifera two P. the of one from inherited erentially the of F excess the and However, 6a), (Figure populations. A. approach angustifolia edge resampling P. our and comm. under core (personal loci between outlier expectation drift of neutral reproducibility genetic high high the the to generating due in arise bias could a This to Buerkle). lead could this form, zones This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted ArticleST h addt Nsfraatv nrgeso norsuyrpeetdgnmcbok pref- blocks genomic represented study our in introgression adaptive for SNPs candidate The eea nihdG em mn h addt oipitt oeta dpiepoessthat processes adaptive potential to point loci candidate the among terms GO enriched Several .balsamifera P. oprdt o-ule oi(iue6) on oitorsinof introgression to point 6b), (Figure loci non-outlier to compared drvdallsi h yrd seiecdb h hf fotirlc oad lower towards loci outlier of shift the by evidenced as hybrids the in alleles -derived eoi akrud(7 fitorsinotir) eurn akrsigmay backcrossing Recurrent outliers). introgression of (47% background genomic eoi akruda eesta xeddmgahcexpectation. demographic exceed that levels at background genomic .balsamifera P. .angustifolia P. tal et ie infiatyi hi eoi intrso oal adaptive locally of signatures genomic their in significantly differ Populus 09 Keller 2009; and tal et .balsamifera P. seas Brunner also (see 21)dmntaearl o 1,3- for role a demonstrate (2011) tal et tal et eeto rvnItorsinin Introgression Driven Selection 03 n hligrqieet(u 2014). (Guy requirement chilling and 2013) .balsamifera P. 01 02.I atclr u phenology bud particular, In 2012). 2011, nti ein n h nihetof enrichment the and region, this in tal et tal et 21)dmntae htrear- that demonstrated (2017) 21).Gvnteextensive the Given (2014)). .angustifolia P. cuisawd geographic wide a occupies .angustifolia P. β .balsamifera P. lcni the in glucan Populus netyinto ancestry noa into vs in study our in association (Suarez-Gonzalez such Manitoba and Alberta Columbia, British the in and in zone species bridization reported pure been in has outliers candidates adaptation selection local introgression between overlap Significant adapta- introgression. local inhibited under loci Similarly, significant. (in not tion were associations those outliers, introgression redox in involved variation allelic of hybrids the in maintenance homeostasis. favor may metal counteract selection to mechanisms levels stress, response the ion biochemical in and molecular decrease of to complexity H the due the given Thus, poplars of in component stress crucial Ex- oxidative a zones. induce Glutathione, hybrid similarly of naturally-occurring also in can selection Zinc under to be posure may traits these that contention the of hybrids in tolerance Cd for to known is example, ula for the exposure, in enzymes Cadmium antioxidative of survival. integrity disruption for the cause essential where toxicity, be ion may metal to homeostasis exposed redox likely of are Mountains Rocky the of soils rich (Sytar metal mechanisms molecules defense a signaling plant important disrupt be can initiate also toxicity to can ROS ROS although 2010). oxygen processes, Tuteja reactive metabolic & important of of amounts (Gill number excess stress of oxidative generation to home- to contributing redox lead (ROS), of can species maintenance cells by the metals and of membranes Absorption cell ostasis. across transport metal and cation involved marginal in present cues environmental of range the from to variants cycling adaptive environments. dormancy of their introgression adapt upon to draw order edge range rear its along This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted adaptation local in involved loci (e.g. neutrality conditional of presence the or regions sympatric Article eodsga ffntoa nihetta a ossetars eso nrgeso outliers introgression of sets across consistent was that enrichment functional of signal second A hl efudoelpbtentegnmcrgoswt vdneo eetv wesadthe and sweeps selective of evidence with regions genomic the between overlap found we While and CHHATRE .alba P. .balsamifera P. (Sch¨utzend¨ubel) tal et and .trichocarpa P. .trichocarpa P. .balsamifera P. tal et 02.Frhroe hr ssbtnilhrtbevariation heritable substantial is there Furthermore, 2002). i o xii eoi sad fdffrnito that differentiation of islands genomic exhibit not did ) tal et and 2 ol eetdffrn eeto eie nallopatric in regimes selection different reflect could O Populus 2 .deltoides P. cvnigmcaim(Tyystj¨arvi mechanism scavenging 03.Orsuyppltosgoigi the in growing populations study Our 2013). x canescens .trichocarpa P. (Induri ope ahbi of hybrid (a complex tal et and 02,wihsupports which 2012), tal et .balsamifera P. .angustifolia P. 08) akof Lack 2018a). tal et .trem- P. 1999). hy- in orlto o nrgeso nopst ieto;fial,ntalo u hrdcniaeoutliers candidate shared our S6). of (Figure regions all subtelomeric not in finally, lie direction; opposite in introgression for for correlation the telomeres of to rest proximity the and introgression to between compared regions subtelomeric in (Wang recombination genome of levels high introgression show adaptive to than appear rather rate recombination high of se per feature genomic shared Suarez-Gonzalez the with overlap to that due study our rates. recombination from high candidates exhibiting the typically Thus for known are which regions subtelomeric in elevated in of rates genome recombination se- in variability natural under genome-wide truly and about are known loci is involved Little the these if hand, lection. re- introgression other high adaptive the facilitate with On also regions introgression. could and adaptive regions genome mimic the that patterns across variable generate may are combination rates Recombination (Martin introgression favor 2017). may Jiggins recombination & of For rates high observed. we undergoing patterns regions genomic genomic the example, generate also may mechanisms biological alternative as liers abiotic and biotic study). to our response in in involved as those stress, oxidative as (including well stress as genes resistance disease for enriched are the In involved. geographically is trichocarpa partner in hybridizing P. shared different be a might when even introgression zones, adaptive hybrid of distant targets are that regions genomic Suarez-Gonzalez that by reported as regions) (7 from introgressing be to zone). hybrid the in selection experience not do range species the in elsewhere This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article neetnl,5 for174itorsinotir r oae nte2 eoi ein found regions genomic 20 the in located are outliers introgression 1,764 our of 54 Interestingly, tl,cuinms eeecsdwe nepeigteaatv infiac fcniaeout- candidate of significance adaptive the interpreting when exercised be must caution Still, .angustifolia P. oee,w n hspsiiiyulkl o eea esn:first, reasons: several for unlikely possibility this find we However, . .trichocarpa P. yrdzn tde ySuarez-Gonzalez by studied zone hybrid tal et u Wang but , 05;scn,Suarez-Gonzalez second, 2015); neetnl Suarez-Gonzalez Interestingly . .balsamifera P. tal et 21)rpr o aito nrcmiainrtsars the across rates recombination in variation low report (2015) noadmixed into tal et 21a.Ti assa nrgigpossibility intriguing an raises This (2018a). eeto rvnItorsinin Introgression Driven Selection tal et .balsamifera P. .trichocarpa P. tal et tal et 21a on nyawa correlation weak a only found (2018a) 21a,itorse eoi regions genomic introgressed (2018a), 21a eotta nrgeso was introgression that report (2018a) nrgesdacsr n no and ancestry introgressed 1 ein)o h opposite the or regions) (13 tal et .trichocarpa P. 21a ol result could (2018a) .balsamifera P. .balsamifera P. Populus osnot does x yrdzto a rvd e oreo dpiegnmcdiversity. genomic adaptive interspecific of and source conditions, key a suboptimal provide under may oppor- persistence hybridization unique population present likely for distribution challenges species’ and a of tunities (Keller range-edge range rear the the of along rest zones the hybrid from Thus, distinct are populations rear-edge in genes phenology refugia species’ glacial of the site (Levsen the near species been environments have this may for inhabit region likely this suggests that modeling Climate Canada limits. and physiological States United the in Mountains (Mimura the species helping the likely of cline, one revealed hybrid other of a the expansion produced northward of that rear-edge oscillations the climatic meet during species introgression one repeated of populations leading where Japan in in noted species been has congener abundant more wintergreen a the with assimilation genetic populations and rear-edge hybridization of extinction through of potential example, dynamics rear- For report the in studies angiosperms. few discussed other a species in explicitly although hybridization tree range, edge that species forest the any of prominent find rear-edge the not in at populations could zones in hybridization and hybrid 2000 of since studies published 200 world over the surveyed We species. tree hybrid of centers be may and 1993), 1997). Elam (Rieseberg & speciation (Ellstrand range the in elsewhere than contact. hybridization of zones other at than evolution, for available material genetic unique have may therefore (Hampe glaciation during refugia al as to served et likely pre-adapted many variants and unique 2005), contain Petit & may (Hampe distribution climates species’ warmer a of rear-edge Marginal the zones. at hybrid populations of maintenance and creation the for opportunities unique present Range-edges Zones Hybrid Range-Edge of Phylogeography (c) This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article nomto nrneeg yrdznsrmissac npat n atclryi forest in particularly and plants in scarce remains zones hybrid range-edge on Information to susceptible more be also may populations marginal size, effective small expected their to Due In CHHATRE 03 eit20;Poa ent 08 eie 01.Hbi oe tterear-edge the at zones Hybrid 2011). Feliner 2008; Bennett & Provan 2004; Hewitt 2003; .balsamifera P. Pyrola tal et h errneeg xssa ueosdsuc ouain ln h Rocky the along populations disjunct numerous as exists range-edge rear the , p.(Beatty spp. tal et 02,adpplto eei tutr swl slclaatto in adaptation local as well as structure genetic population and 2012), tal et 00.I nte td,caecn oeso two of models coalescent study, another In 2010). tal et 2014). tal et 2017). Rubus n eonz u aeclegeadfin,Cr .Dulso nvriyo rts oubafor Columbia British of remember University to of Douglas like J. would We Carl friend, in manuscript. and interest the colleague twohis improve late from our helped Comments recognize Lexer #1461868. and Award C. Foundation and Science reviewers National by anonymous supported was study This Acknowledgements with contact, evolution. adaptive secondary their upon for introgression so, implications by If followed important divergence as lineage species. such of these episodes trees between repeated forest contact by outbreeding secondary highly ancient of more introgression history the ancestral of evolutionary of involving relict the some events a whether flow be speculate to may gene interesting here for is uncovered it support Thus, was 3). there Figure and (e.g., populations millennia, for persist recent relatively may from that result to backcrosses), recent appear selection- and genotypes for F2, hybrid (F1, context admixture the historical of a many introgressed provides While with studies outliers introgression. other driven introgression in the individuals introgression hybrid of of in some patterns regions of shaping genomic Overlap in Signatures populations. active range-edge been genomes. these has parental in selection pure indicate in formation introgression occurring the adaptive otherwise of through not persistence combinations population genotypic novel facilitate of may positions range-edge in hybrid of Formation complexes incomplete/weak hybridization. by interspecific evidenced extensive and genomes, species permeable between with barriers reproductive complex species a represent to seem thus these hybrids. between generation commonplace advanced and be early to both appears including Hybridization lineages, in Rockies. complex the hybrid in overlap tri-species of a zone sympatric of presence the demonstrate results Our Conclusions 5. This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article Populus nrgesv yrdzto n epu icsin bu hsstudy. this about discussions helpful and hybridization introgressive Populus eeto rvnItorsinin Introgression Driven Selection r nw ofr oglvdvgttv clones vegetative long-lived form to known are Populus Populus nsect. in Populus a echaracterized be may Tacamahaca hogotthe throughout Populus would cewle E(94 aua nescinlhbiiainbtennrhaeia pce of species american north between hybridization intersectional Natural (1984) JE Eckenwalder CP, a Joshi in GT, Slavov SP, selection DiFazio exogenous and Adaptation (2014) SN Aitken B, Jaquish T, Wang AR, Torre La De G, Abecasis A, Auton introgression P, massive Danecek invasions: of side hidden The (2008) L Excoffier RJ, Petit M, Ruedi M, Currat L, script. Bresadola St¨olting KN, plotting C, Christe admixture modified A 2.3: Distruct (2018) VE Chhatre to requirement A, chilling Soto V, the Storme and MT, Vernalization Cervera (2014) X Sheng CY, Hsu LM, boundary: Evans range AM, species Brunner a at hybridization Unidirectional (2010) J Provan M, Philipp GE, Beatty Center, zones. hybrid Computing of Analysis Research (1985) Advanced GM Hewitt Cluster, NH, Barton X using System hybrids IBM species Moran: identifying Mount for (2012) method ARCC model-based A (2002) E Thompson unrelated E, in ancestry Anderson of estimation model-based Fast (2009) K Lange J, Novembre DH, Alexander References 6. This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted taxonomy. ii. tacamahaca. and aigeiros sections Botany in NH: Enfield, (salicaceae) poplar. populus of breeding and genomics Genetics, editors. C, Kole Publishers Science SP, Difazio C, Joshi change. glauca picea 27 genes. local by flow. gene recurrent and fertility f1 despite species ecology populus Molecular hybridizing in isolation reproductive distruct2.popgen.org markers. aflp on based 1440–1456. populus genus the in relationships regulation? separate or shared Article dormancy: bud exit tracking. habitat for implications 113–148. pp. http://n2t.net/ark:/85786/m4159c. doi: WY. Laramie, Wyoming, of University data. genetic multilocus individuals. 2156–2158. , CHHATRE , e Phytologist New 62 325–335. , × eoeresearch Genome ie nemni yrdzn:ipiain o oetmngmn ne climate under management forest for implications zone: hybrid engelmannii picea tal et Evolution , p 1–28. pp. , 25 . 2482–2498. , , Genetics , 201 62 1908–1920. , , 687–699. , tal et 19 tal et tal et , 1655–1664. , iest n Distributions and Diversity 160 20)Itapcfi n neseicgntcadphylogenetic and genetic interspecific and Intraspecific (2005) tal et 21)Ppls rme ine ytmfrpatgenomics. plant for system pioneer premier a Populus: (2011) 21)Tevratcl omtadvcftools. and format call variant The (2011) 1217–1229. , 21)Slcinaantrcmiathbismaintains hybrids recombinant against Selection (2016) r nir npatscience plant in Frontiers nulrve fEooyadSystematics and Ecology of review Annual hoeia n ple Genetics Applied and Theoretical , 16 1–9. , vial rmhttp:// from Available aainJunlof Journal Canadian , 5 732. , Bioinformatics , 111 , , , opr ,BekeA 20)Apwru ersinbsdmto o ditr apn of mapping admixture for method regression-based powerful A (2009) AC Buerkle Z, Gompert F, Lu tol- TM, stress Casstevens abiotic in JC, machinery Glaubitz antioxidant and species oxygen Reactive (2010) N Tuteja SS, Gill both for CJ, appropriate Grassa loci N, Farzaneh selected A, identify Geraldes to method genome-scan A (2008) interactions O Plant–herbivore Gaggiotti (2016) M, TG Foll Whitham N, Isabel MK, Lau J, that Godbout populus KD, of Floate species three the among hybridization of patterns and Extent (2004) KD the Floate to contributing incompatibilities dobzhansky-muller for Evidence tales. (2001) of JH tale Willis a L, Fishman refugia: glacial european Southern (2011) expansions. GN range Feliner of consequences Genetic (2009) RJ Petit M, Foll L, Excoffier E, Rodgers-Melnick GT, Slavov LM, Evans DW, Pearce S, Kaluthota LM, Evans herbivorous the in divergence drive hosts hybrid Populus (2012) TG Whitham GJ, Allan LM, Evans SP, DiFazio GJ, Allan LM, Evans Q, Sun JC, Glaubitz implica- RJ, size: Elshire population small of consequences genetic Population (1993) DR Elam NC, Ellstrand This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted hybrids. of genome the across isolation pipeline. analysis quencing plants. crop in population erance of patterns shaping in selection natural and flow, gene structure. limited hybridization, of role perspective. bayesian bridges, a hybrid markers: codominant of and hypotheses dominant for support assessing populus: similarity. of genetic and swarm novelty hybrid evolutionary trispecific a in canada. alberta, southern of forest 253–264. riparian the constitute nasutus. m. and guttatus mimulus between hybrids of sterility Systematics and Evolution, Ecology, Article associations. trait adaptive and selection of signatures identifies across adaptation impact arthropods. and associated angustifolia and populus range in distributional gradient the latitudinal a across selection gent habitat. essential as zones hybrid plant of conservation Genetics for Conservation implications parapopuli: aceria mite, cottonwoods. narrowleaf in history graphic species. diversity high for approach conservation. plant for tions Evolution , 68 ln hsooyadbiochemistry and physiology Plant , 13 3260–3280. , 1601–1609. , LSOne PLoS nulrve fEooyadSystematics and Ecology of review Annual tal et tal et tal et tal et tal et , lSone PloS 40 , 21)Gorpia aresadciaeiflec demo- influence climate and barriers Geographical (2015) 21)Arbs,sml eoyigb-eunig(gbs) genotyping-by-sequencing simple robust, A (2011) 9 oeua Ecology Molecular 481–501. , 21)Lnsaegnmc fpplstihcra the trichocarpa: populus of genomics Landscape (2014) e90346. , tal et 21)Bdpeooyadgot r ujc odiver- to subject are growth and phenology Bud (2016) 21)Tse-b:ahg aaiygntpn yse- by genotyping capacity high a Tassel-gbs: (2014) Heredity e Phytologist New , 21)Pplto eoiso ouu trichocarpa populus of genomics Population (2014) 6 e19379. , eeto rvnItorsinin Introgression Driven Selection , clg n Evolution and Ecology 114 , 387–396. , , 48 18 , 909–930. , Genetics aainJunlo Botany of Journal Canadian 209 1207–1224. , Evolution auegenetics Nature 832–844. , Taxon , 180 , 24 , , 55 . 60 977–993. , 217–242. , 1932–1942. , 365–372. , nulRve of Review Annual , 46 Populus 1089–1096. , , 82 , eitG(04 eei osqecso lmtcoclain ntequaternary. the in oscillations climatic of consequences Genetic (2004) of G patterns Hewitt and admixture of analysis Genetic (2014) TG Whitham GJ, Allan EI, and Hersch-Green introgression, differential divergence, genome Heterogeneous (2016) EL Larson RG, boundaries. Harrison species of nature the and introgression, Hybridization, (2014) EL Larson RG, Harrison sequences nucleotide on based (salicaceae) populus of matters. Phylogeny edge (2004) S rear Dayanandan the M, Hamzeh change: climate under biodiversity Conserving (2005) future. RJ Petit present, A, past, Hampe relicts: Climate (2011) AS Jump A, bird-dispersed a Hampe of phylogeography Rangewide (2003) RJ Petit P, Jordano J, for Arroyo genes A, Hampe candidate reveals introgression Differential (2013) SN Aitken C, Lexer warm. JA, to Hamilton gets bud early The (2014) frequencies. RD allele Guy from adaptation local of identification Robust (2013) G coloniza- Coop G¨unther historical T, of patterns Contrasting (2006) VL Sork techniques. RJ, new Petit M, ideas, DEGUILLOUX old D, Grivet plants: in Hybridization challenges (2017) R and Hopkins truths F, enduring Roda hybrids: BE, Goulet are anything, if What, (2016) CA Buerkle clines. Z, genomic Gompert of estimation Bayesian (2011) AC Buerkle Z, isolation Gompert of components mapping for package software a Introgress: (2010) AC Buerkle Z, Gompert This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted Sciences Biological B: London of Society Royal the of Transactions usa. colorado, southwestern in (salicaceae) Genomes trees & cottonwood Genetics foundation in introgression zones. hybrid of structure and origin the Heredity of Journal rdna. nuclear and region trnt-trnf chloroplast of letters Ecology Systematics and Evolution, refugia. glacial temperate and 3415–3426. mediterranean contrasting shrub: eurasian sitchensis (picea 938. spruce a across selection Articlenetics europe. and california in spp.) (quercus oaks white in tion Physiology flow. gene and structure population with associated 2111–2127. hybrids. in CHHATRE , 195 , 205–220. , oeua clg Resources Ecology Molecular 173 , tal et 8 65–78. , 461–467. , , 105 , 10 795–809. , 527–539. , , 42 313–333. , , × oeua ecology Molecular 10 e Phytologist New .gac)hbi zone. hybrid glauca) p. 378–384. , mrcnjunlo botany of journal American vltoayApplications Evolutionary . oeua Ecology Molecular , 202 7–9. , , nulRve fEcology, of Review Annual e Phytologist New 359 183–195. , oeua Ecology Molecular oeua Ecology Molecular , , 91 15 . 1398–1408. , 4085–4093. , Philosophical , 197 927– , Plant , , Tree Ge- 12 20 , , iuaM ihm ,LsoxM aaaT(04 ag hf n nrgeso fterear the of introgression and shift Range (2014) T Yahara M, Lascoux M, Mishima M, Mimura MC, Gros-Louis M, Lamothe PG, Meirmans gene Kl´apˇstˇe RD, filter AD, Guy selectively McKown populations J, Hybrid (2001) P Keim RJ, Turek TG, Whitham GD, Martinsen introgression. of landscape genomic the Interpreting (2017) CD Jiggins parameteriza- SH, neutral Martin and history demographic of Evaluation seedlings (2014) MC populus Whitlock of KE, Lotterhos ancestry Unexpected (2014) CA Buerkle C, Lexer transform. Z, burrows–wheeler with Gompert alignment D, read Lindtke short accurate and Fast (2009) R Durbin H, Li M, (salicaceae). Loo populus van genus JA, the Joseph in C, speciation Lexer Pleistocene (2012) MS Olson P, Tiffin ND, Levsen Climate- (2011) L, P Holeski MA, Tiffin Bowker L, MS, Lamit Olson SN, Silim RD, Guy RY, Soolanayakanahally SR, network gene Keller flowering-time the adaptive in adaptation locally Local (2012) on P Tiffin position MS, Olson range N, Levsen of SR, Keller Influence (2017) MC Fitzpatrick of swarm VE, hybrid Chhatre interspecific an SR, of Keller analysis Genetic (1989) K Lark T, Whitham K, Paige P, Keim GT, Slavov DR, Ellis BR, Induri This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted species. rubus distinct ecologically two in 14 populations leading and species. poplar american north native and exotic trichocarpa. populus of populations natural in variation Phytologist trait ecological underlying genes species. between introgression development & genetics in tests. outlier fst of species. performance of the maintenance on the tion in selection postzygotic for role large a ecology implies Molecular zone hybrid a from Bioinformatics mating. and isolation reproductive of patterns unexpected reveals spp. Article biology Systematic lichen. bark dominant a influences species tree balsamifera populus poplar, balsam in phenology and ecophysiology l.(salicaceae). of adaptation local driven l. balsamifera populus poplar, balsam of genes. time flowering populus in associations gene–environment introgression. unidirectional of occurrence populus: populus. in tolerance cadmium for genes 209. , , 203 mrcnJunlo Botany of Journal American , 25 535–553. , , , 23 1754–1760. , 61 4316–4330. , 401–412. , , 47 69–74. , Evolution tal et tal et tal et tal et 21)Ietfiaino uniaietatlc n candidate and loci trait quantitative of Identification (2012) 21)Gntclybsdtatvrainwti foundation a within variation trait Genetically-based (2011) 21)Gnmcamxueaayi nerpa populus european in analysis admixture Genomic (2010) , 21)Gnm-ieascainipiae numerous implicates association Genome-wide (2014) oeua ilg n Evolution and Biology Molecular rephysiology Tree tal et 55 , oeua ecology Molecular 1325–1335. , 98 21)Cmlxpten fhbiiainbetween hybridization of patterns Complex (2010) 99–108. , uglEcology Fungal eeto rvnItorsinin Introgression Driven Selection mrcnJunlo Botany of Journal American Genetics , 32 626–638. , , , 123 , 23 ora fHeredity of Journal 4 103–109. , 2178–2192. , 557–565. , M vltoaybiology evolutionary BMC Genetics , 29 3143–3152. , , 97 urn opinion Current , 186 1688–1697. , Populus , 109 699–712. , 47–58. , New , ttlrR sff ,W 19)Terl fhbiiaini h eei aiuaino populus. of manipulation genetic the in hybridization of role The (1996) R Wu L, Zsuffa R, Stettler assimi- Enhanced (2009) WR Schroeder EC, Drewes SN, Silim RD, speciation. Guy RY, plant Soolanayakanahally in hybridization of role The (2009) DE Soltis PS, Soltis h and Cadmium (2002) A Polle C, Sch¨utzend¨ubel Rudolf P, Nikolova A, J, Vahala A, Welling PL, Rinne DM, Rosenthal O, Raymond LH, Rieseberg RA, Randell SC, Kim LH, Rieseberg species. plant of origins Hybrid (1997) LH Rieseberg structure population of inference variational faststructure: (2014) JK Pritchard M, Stephens A, Raj refugia. glacial cryptic into insights genome-wide Phylogeographic (2008) from K mixtures Bennett and J, Provan splits population of Inference (2012) JK Pritchard JK, Pickrell JL, Beaulieu de I, Aguinagalde RJ, Petit P, Pavlidis RY, Soolanayakanahally for N, scans Levsen Genomic (2005) MS, C Olson Bustamante AG, Clark MJ, Hubisz Y, Kim S, Williamson R, Nielsen This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted conservation and management for implications its and Populus of Biology and l.). capacity balsamifera photosynthetic increased (populus through 1821–1832. poplar latitude balsam with in efficiency conductance use internal water and rate lation biology populus in 3- 1, populus. ga-inducible recruits and t hybridization. by facilitated flowers sunflowers. annual by habitats 28 sets. data snp large in Article evolution & data. frequency allele diversity. genetic of pots genomes. of thousands in sweeps selective climate. global warmer a in requirements phenology 1214–1230. to l. balsamifera data. snp using sweeps selective 359–389. , CHHATRE , 60 h ln Cell Plant The ikv´ ,Saaai ,Aahoi 21)Sed ieiodbsddtcinof detection likelihood-based Sweed: (2013) N Alachiotis A, Stamatakis Zivkovi´c D, ˇ × 561–588. , , 23 aecn roots. canescens tal et 564–571. , LSGenet PLoS Genetics , science 23 130–146. , tal et ln hsooyadBiochemistry and Physiology Plant Genetica , β , eoeresearch Genome 197 guaae oroe inlcnut n ees omnyin dormancy release and conduits signal reopen to -glucanases 300 , 21)Ciln fdratbd yeidcsflwrn locus flowering hyperinduces buds dormant of Chilling (2011) 8 Science 573–589. , e1002967. , tal et 1563–1565. , , tal et 129 tal et oeua ilg n evolution and biology Molecular 20)Hbiiainadteclnzto fnovel of colonization the and Hybridization (2007) , 301 149–165. , 20)Gailrfga ososbtntmelting not but hotspots refugia: Glacial (2003) tal et 20)Mjreooia rniin nwl sun- wild in transitions ecological Major (2003) 1211–1216. , , 15 nulrve fEooyadSystematics and Ecology of review Annual 21)Teaatv oeta fpopulus of potential adaptive The (2013) 1566–1575. , ln,Cl Environment & Cell Plant, , 40 2 577–584. , o 2 idcdoiaiestress oxidative -induced oeua Ecology Molecular nulrve fplant of review Annual p 87–112. pp. , , 30 2224–2234. , r nsi ecology in Trends , , 32 22 , , , ofJ,Elge 21)Mkn es fgnmcilnso ieetaini ih fspeciation. of light in differentiation of islands genomic in of hybridization sense Making of (2017) Patterns H (2010) Ellegren JB, MS Wolf King LP, Albert LG, Campbell JR, Ahern KD, Whitney structure. JA, population Schweitzer JK, of Bailey analysis TG, the Whitham for f-statistics Estimating (1984) CC Cockerham BS, Weir rate recombination and selection Natural (2015) PK Ingvarsson DG, Scofield NR, Street J, Wang of Photoinhibition (1999) CH Foyer L, Jouanin R, Kettunen ACM, Arisi M, Riikonen Tyystj¨arvi E, S, Jansson S, Difazio GA, Tuskan variable The (2010) PK Tucker MW, Nachman CA, Buerkle populus Z, Gompert native LM, and Thibodeau KC, Teeter poplars exotic When (2012) N Isabel J, Bousquet WR, genome-wide Schroeder of P, analysis Talbot functional Snp2go: (2014) M Gallach A, Haeseler von M, Kapun D, Szkiba metal-induced Heavy (2013) M Prasad K, Strza P, lka Kuczynska D, Latowski A, Kumar O, Sytar Boˇsnjak M, F, Supek perspective. plant a introgression: of adaptive (2018b) direction QC Cronk and C, Lexer Scale A, Suarez-Gonzalez (2018a) CJ Douglas QC, Cronk C, Lexer CA, Hefer A, Suarez-Gonzalez C, Christe CA, Hefer A, Suarez-Gonzalez This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted Genetics Reviews Nature plants. ecosystems. to genes from genetics: species. Evolution populus related three of genomes the across Genetics polymorphism nucleotide shape variation overexpressing poplars and reductase dismutase. glutathione overexpressing superoxide plants tobacco in ii photosystem gray). & (torr. mice. house of species hybridizing 485. between isolation of architecture of genomic establishment and hybridization Spontaneous prairies: canadian the hybrids. interspecific on meet l. balsamifera Article studies. association plants. in mechanisms detoxification and plantarum reactions, defense damage, oxidative terms. ontology Letters ( cottonwood balsamifera black between introgression adaptive from cottonwood). introgression adaptive of case , esetvsi ln clg,EouinadSystematics and Evolution Ecology, Plant in Perspectives 14 p genetics–115. pp. , , , . 38 ). 35 1358–1370. , oeua ecology Molecular oeua ecology Molecular 985–999. , science lSone PloS knaN, Skunca ˇ Genetics oeteooyadmanagement and ecology Forest , hsooi Plantarum Physiologia 313 , , 18 6 1596–1604. , e21800. , , 87. , mcT(01 eiosmaie n iulzsln it fgene of lists long visualizes and summarizes Revigo (2011) T Smuc ˇ 197 tal et , . 27 285–289. , 1667–1680. , ouu balsamifera populus 20)Tegnm fbakctowo,pplstrichocarpa populus cottonwood, black of genome The (2006) aueRvesGenetics Reviews Nature tal et tal et 21)Gnmcadfntoa prahsrva a reveal approaches functional and Genomic (2016) 20)Afaeokfrcmuiyadecosystem and community for framework A (2006) , 105 eeto rvnItorsinin Introgression Driven Selection 409–416. , ouu trichocarpa Populus , 285 bla olr in poplar) (balsam 142–152. , , 7 510–523. , , 12 175–182. , n asmppa ( poplar balsam and ) .trichocarpa p. Evolution caphysiologiae Acta Populus , 64 Biology (black 472– , p. huL aaR oldyJ(04 xm eeunigrvassgaue fdmgahcand demographic of signatures reveals resequencing Exome (2014) J Holliday R, Bawa L, their Zhou and relicts Climate (2014) JK Bailey GJ, Allan CA, Gehring TG, Whitham SA, Woolbright This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved.

Accepted Article trichocarpa). (populus cottonwood black of range and genome ecology the Molecular across processes adaptive laboratories. evolution and ecology lution natural as communities associated CHHATRE , 29 406–416. , tal et , 23 2486–2499. , rnsi clg evo- & ecology in Trends l uhr edtefia manuscript. final contributed the and LME read LME authors drafts. manuscript. earlier All on the feedback wrote extensive angustifolia and provided and analysis P. manuscript data of performed parts study, wrote the SDF conceived SRK and VEC Contributions https://cryptic0.github.io/HybridPoplar.Author at files input located All repository SRP070954. github number the accession in SRA archived NCBI been through available have is data sequence raw All Archiving Data This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article ape.SFadLEpoie eoi aao v additional five on data genomic provided LME and SDF samples. eeto rvnItorsinin Introgression Driven Selection Populus Populus species. ito Tables of List Tables 7. This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article EHBISaayi fgntp sinet ausaetenmeso indi- of numbers the are Values assignment. genotype of analysis NEWHYBRIDS for 2 localities Sampling 1 itiuino eoyi lse tcniaeSP o ieeta nrgeso in- introgression differential for SNPs candidate at classes genotypic of Distribution 3 CHHATRE yrd 35 ...... separate . two from on . populations based in . are Results hybrids . markers. generation . SNP advanced 375 . and from . inferred F2 zones . F1, sympatric . to . assigned viduals . . . . hybrids iia rbblte fgntp sinet...... 36 ...... ( . deficit . and (+), . excess . (=), . expectation per . INTROGRESS proportions of . run single a . from ferred . . assignments. population, genotype parental of single probabilities a similar into poplars excluding balsam second the and combining first with analyses, tal et .trichoarpa P. .angustifolia P. rmteaayi,bt fwihyeddhighly yielded which of both analysis, the from , .balsamifera P. vs 0 ottapdrn.Ky Genotypic Key: runs. bootstrapped 100 , .trichocarpa P. − ...... 37 ...... ). n putative and , This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. ypti BLA RMP PBALSAM MSG Sympatric PBALSAM JKH Sympatric PBALSAM Sympatric loarcPRCOOYPCOypcPnnua A34.8 -122.900 47.589 WA River, Thirteen 3 WA Skagit, THIRTEEN WA Skykomish, PTRICHO SKYKOMISH WA PTRICHO Allopatric Puyallup, SKAGIT WA Peninsula, Olympic PTRICHO Allopatric PUYALLUP ON PTRICHO WAAllopatric River, OLYMPIC Nooksack, White WA PTRICHO Allopatric River, NOOKSACK Nisqually -102.593 PTRICHO Allopatric NISQUALLY 49.876 PTRICHO Allopatric WTR PBALSAM 14 Allopatric UMI PBALSAM Allopatric TUR -111.736 PBALSAM Allopatric TIM SK Area, PBALSAM Allopatric 35.013 Mtn. SKN Moose PBALSAM Allopatric RAD 2 PBALSAM Allopatric OFR UT River, Weber PBALSAM Allopatric UT MMT Creek, Oak PBALSAM Allopatric CPL AZ Wash, Pumphouse PBALSAM Allopatric AZ UTWR River, Blue PANGUST Allopatric UTAH Location PANGUST Allopatric AZPW PANGUST Allopatric AZBR Popcode PANGUST Allopatric Allopatric Species zone Geog. Accepted -125.065 WY River, Snake 49.706 CYH CO PBALSAM 8 NP, AB SSR Mtn. River, Rocky Oldman Sympatric PBALSAM WYSR Sympatric PANGUST RMPANG WA Sympatric River, PANGUST One ABOR Thirty Sympatric PANGUST THIRTYONE PTRICHO Sympatric Allopatric Article al 1 Table PANGUST: apiglclte for localities Sampling .angustifolia P. PBALSAM: ; .angustifolia P. .balsamifera P. ok t.N,CO NP, Mtn. Rocky WY Gulch, Mosier WY Hole, Jackson mua,QC Umiujaq, SK Turtleford, ON Timmins, SK Saskatoon, QC Radisson, ON Chapleau, hehn ie,W 64.6 -109.610 44.462 16 SK PP, Hill Cypress WY River, Shoeshone vrFoigRvr B1 315-101.101 53.145 15 MB River, Flowing Over , .balsamifera P. eeto rvnItorsinin Introgression Driven Selection PTRICHO: ; , .trichocarpa P. .trichocarpa P. .Id aiueLongitude Latitude Ind. N. 35.0 -108.348 53.203 13 34.3 -109.806 49.636 13 64.5 -105.563 -106.873 40.252 44.323 16 15 24.8 -85.276 48.587 12 -81.633 -106.613 48.363 52.337 14 14 44.2 -110.477 43.825 14 45.2 -77.641 53.429 14 -83.262 47.516 14 14.4 -111.380 40.848 31 635-76.255 56.335 4 -111.630 38.713 3 971-113.099 49.791 -128.600 5 -121.837 54.150 -122.079 47.832 2 48.511 8 8 370-109.052 33.730 2 322-110.869 -105.627 43.242 40.401 5 6 -122.203 47.086 -122.173 8 -122.636 48.804 47.104 8 9 n uaiehybrids putative and , Populus Accepted Article yrd nppltosfo ypti oe nerdfo 7 N akr.Rslsaebsdo w eaaeaaye,wt rtcombining first excluding with second analyses, separate and two population, on based assignments. parental are genotype single Results of a markers. probabilities SNP into similar 375 poplars from inferred balsam zones the sympatric from populations in hybrids 2 Table EHBISaayi fgntp sinet ausaetenmeso niiul sindt 1 2adavne generation advanced and F2 F1, to assigned individuals of numbers the are Values assignment. genotype of analysis NEWHYBRIDS CFxA F2 F2 F1 F1 BC-F2xBAL BC-F2xANG BC-F1xBAL BC-F1xANG F2 F1 Cross BAL ANG Class Genotype BC-BALx(F2xBAL) BC-ANGx(F2xANG) BC-BALx(F1xBAL) BC-ANGx(F1xANG) ∗ o h eodaayi where analysis second the For This article is protected by copyright. All rights reserved. This article is protected rights by All copyright. reserved. .balsamifera P. angustifolia P. balsamifera P. angustifolia P. F1 x F1 angustifola P. balsamifera P. angustifolia P. x x x x .balsamifera P. angustifolia P. balsamifera P. angustifolia P. .trichocarpa P. x ( ( x ( x ( x ( x ( a A .balsamifera P. ) ) F2 F1 niiul rmtepplto RMP. population the from individuals F2 F1 x x x x .balsamifera P. balsamifera P. .angustifolia P. angustifolia P. ape eeecue,rslscudntb bandfr2hybrid 2 for obtained be not could results excluded, were samples .2 .2 .2 0.625 0.75 0.125 0.125 0.125 0.125 0.125 ) 0 ) .2 .2 .2 0.125 0 0.125 0.125 0.125 0.125 0.625 ) 0.75 ) 0 0 0 1 AA Aaa aA Aa AA .50150150.5 0.5 0.25 0.125 0 0.125 0.25 0 0.25 0.125 0.25 0.125 0.25 0.5 0.25 0.25 0.25 0.5 0.25 0.5 0 0.5 0.25 0 1 0 0 0 .trichoarpa P. x.Acsr rprin .inds. N. Proportions Ancestry Exp. oa ubro Individuals of Number Total rmteaayi,bt fwihyeddhighly yielded which of both analysis, the from ∗ observed

90 48 22

9 1 3 0 0 3 0 3 0 1

tal et CHHATRE Accepted Article ottapdrn.Ky eoyi rprin e xetto =,ecs +,addfii ( deficit and (+), excess (=), expectation per proportions Genotypic Key: runs. bootstrapped 3 Table A a aa+ Aa+ AA+ aa= Aa= AA= Explanation Code Genotype A a aa- Aa- AA- A a aa+ Aa= AA+ A a aa+ Aa- AA+ A a aa- Aa- AA+ aa- Aa+ AA+ aa- Aa= AA+ A a aa= Aa+ AA+ aa= Aa= AA+ A a aa= Aa- AA+ A a aa+ Aa+ AA- aa+ Aa= AA- A a aa- Aa+ AA- aa+ Aa- AA- A a aa- Aa= AA- A a aa= Aa- AA- aa= Aa+ AA- aa= Aa= AA- A a aa+ Aa= AA= A a aa+ Aa+ AA= A a aa- Aa= AA= aa+ Aa- AA= A a aa- Aa- AA= aa- Aa+ AA= A a aa= Aa- AA= A a aa= Aa+ AA= itiuino eoyi lse tcniaeSP o ieeta nrgeso nerdfo igerno INTROGRESS of run single a from inferred introgression differential for SNPs candidate at classes genotypic of Distribution This article is protected by copyright. All rights reserved. This article is protected rights by All copyright. reserved. l oeta expected than more All expectation per All Total l esta expected than less All oeAG x es oeBAL More Hets, exp ANG, More oeAG esHt,Mr BAL More Hets, Less ANG, More oeAG esHt esBAL Less , Hets Less ANG, BAL More Less Hets, More ANG, BAL More Less Hets, Exp ANG, More oeAG oeHT,EpBAL Exp HETS, More ANG, BAL More exp Hets, exp ANG, More oeAG esHt,EpBAL Exp Hets, Less ANG, More esAG oeHt,Mr BAL More Hets, More ANG, BAL Less More Hets, exp ANG, Less esAG oeHt,Ls BAL Less Hets, More ANG, BAL Less More Hets, Less ANG, Less esAG x es esBAL less Hets, exp ANG, Less esAG esHt,EpBAL Exp Hets, Less ANG, BAL Less Exp Hets, More ANG, BAL Less exp Hets, exp ANG, Less x N,epHt,Mr BAL More Hets, exp ANG, Exp x N,Mr es oeBAL More Hets, More ANG, Exp x N,epHt,Ls BAL Less Hets, exp ANG, BAL Exp More Hets, Less ANG, Exp x N,Ls es esBAL Less Hets, Less ANG, BAL Exp Less Hets, More ANG, Exp x N,Ls es x BAL Exp Hets, Less ANG, Exp x N,Mr es x BAL Exp Hets, More ANG, Exp f32 ecn f16 Percent 1764 Of Percent 3723 Of u ie run 1 sites Num 3723 104 5 12.33 459 4 17.22 641 5 17.67 134 658 123 0 13.48 502 5 12.19 112 454 304 125 15 21 11 24 21 0 0 0 0 0 0 0 0 0 9 6 − ). 2.79 0.56 3.01 0.64 8.17 0.24 3.36 0.16 0.56 0 0657.60 1016 100 0.4 3.6 3.3 0.3 0 0 0 0 0 0 0 0 0 u ie 0 runs 100 sites Num 4 13.72 242 117 8 16.38 289 4 14.00 247 19 35 20 22 0 0 0 0 1 0 1 0 2 0 0 0 0 9 0 3 0 0 9 0.06 0.00 0.11 0.00 0.00 0.00 1.08 0.00 1.98 6.63 0.00 0.06 0.17 0.00 0.00 1.13 0.00 0.00 0.00 0.51 0.00 1.25 0.51 0.00 vs

100

eeto rvnItorsinin Introgression Driven Selection Populus ito Figures of List Figures 8. This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. Accepted Article eoyi lseigfo DITR.Clr orsodt netycontribu- ancestry to Rocky correspond the Colors in ADMIXTURE. overlap from of clustering area Genotypic and ranges species showing localities sampling 2 of Map 1 EIOmlidmninlsaigpo fGn nooy(O em enriched terms (GO) Ontology Gene of plot scaling multi-dimensional REVIGO 7 Or- resamples. bootstrap 100 on based results INTROGRESS of Reproducibility (a) 19 the for 6 ancestry genotypic species-specific of probability showing plot Ancestry between heterozygosity interspecific 5 of plot Triangle arrows Colored 4 events. migration and splitting population of analysis TREEMIX 3 CHHATRE onansmarczn 39 ...... and . species parental . from . tion . . zone sympatric Mountain au ftets o ucinlercmn fSP hwn ieeta nrgeso.45 introgression. differential -log10P showing the SNPs to of proportional enrichment is functional size Circle for of on test matrix). uniqueness the similarity based greater of the terms value a in term reflect redundant GO colors minimally given (warmer a show terms similar Points 40 semantically clustering outliers. . introgression . 41 among . . . . . bootstrap . of . (orange) all in loci . distribution . introgression candidate Density adaptive . . for (b) . candidates . were . runs. that . loci . . depicts . bar . ange . . . . Orange . . index. . hybrid . in . . varying balsamifera . individuals . of . . represent range . regions . a . across . chromosomes . . poplar . . . For . . . routes. . migration . and . 7-10 . 0) . (d): . through . (a) S3. . Figure flow. . Supplementary gene see . residuals, of . magnitude . population the dicating . from events . migration zone . represent hybrid . the and . labels), . orange and . lightgreen labels) (darkgreen, (blue species pure per one .trichocarpa P. .balsamifera P. tal et lk eoye ( genotypes -like .angustifolia P. lgtgen.Pplto ae oosrpeettetrezones, three the represent colors label Population green). (light hbi ne )...... 42 ...... 1) = index (hybrid vs .balsamifera P. 92nua oi(ry...... 44 ...... (gray). loci neural 1912 aa n lerpeet neseichtrzgts( heterozygotes interspecific represents blue and ) lk eoye ( genotypes -like F ST in dr green), (dark .angustifolia P. i opopulation to AA ,drgenrgosrepresent regions darkgreen ), .angustifolia P. .angustifolia P. eie lee rm1764 from alleles derived j ihclrrm in- ramp color with hbi ne = index (hybrid oag,blue), (orange, Aa P. .43 ). Accepted Article

Latitude 45 50 55 35 40 iue1 Figure THIRTY − ● ONE 130 NISQUALLY OLYMPIC Putative hybrids P. angustifolia P. trichocarpa P. balsamifera ● a fsmln oaiissoigseisrne n rao vra nteRcyMuti ypti zone sympatric Mountain Rocky the in overlap of area and ranges species showing localities sampling of Map THIRTEEN This article is protected by copyright. All rights reserved. This article is protected rights by All copyright. reserved. ● ● ● ● ● ● ● NOOKSACK − 120 PUYALLUP SKAGIT SKYKOMISH UTWR UTAH AZPW WYSR ABOR ● JKH ● ● ● − ● TUR SSR ● 110 ● CYH ● ● ● AZBR ● ● SKN MSG ● ● Longitude MMT RMPANG RMP ● − ● OFR 100 − 90 0 scale approx 1:32,000,000 200 WTR ● 400 ● CPL 600 km ● − TIM 80 ● RAD

●

UMI

eeto rvnItorsinin Introgression Driven Selection Populus Accepted Article drgen ihgenadoag aes,adtehbi oe(lelabels) (blue zone hybrid the and labels), orange and lightgreen (darkgreen, green), 2 Figure .angustifolia P. eoyi lseigfo DITR.Clr orsodt netycnrbto rmprna species parental from contribution ancestry to correspond Colors ADMIXTURE. from clustering Genotypic oag,bu) and blue), (orange, This article is protected by copyright. All rights reserved. This article is protected rights by All copyright. reserved. .trichocarpa P. lgtgen.Pplto ae oosrpeettetrezns n e uespecies pure per one zones, three the represent colors label Population green). (light (b) (a) (c) K K K =4 =2 =3 .balsamifera P.

(dark

tal et CHHATRE hog d:71 irto ots o eiul,seSplmnayFgr S3. Figure Supplementary see residuals, For routes. migration 7-10 (d): through population from events gration 3 Figure This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. 0.0 0.0

Accepted10 s.e. weight Migration Article10 s.e. weight Migration 0 0.5 0 0.5 DELTOIDES DELTOIDES 0.1 REI nlsso ouainsltigadmgaineet.Clrdarw ersn mi- represent arrows Colored events. migration and splitting population of analysis TREEMIX 0.2 (a) 7Migration Routes (c) 9Migration Routes JKH MSG SSR THIRTEEN THIRTY_ONE SKYKOMISH NOOKSACK OLYMPIC 0.2 SKAGIT PUYALLUP NISQUALLY CYH TIM SKN TUR WTR CPL RAD UMI OFR MMT RMP Drift parameter Drift parameter Drift THIRTEEN OLYMPIC SKAGIT SKYKOMISH THIRTY_ONE NOOKSACK PUYALLUP NISQUALLY JKH 0.3 0.4 MSG SSR OFR CYH TUR TIM SKN MMT WTR CPL UMI RAD RMP i opopulation to 0.4 Putative hybrids P. trichocarpa P. balsamifera P. angustifolia AZBR AZPW 0.6 ABOR UTAH Var. Expl:99% Var. Expl:99% RMPANG WYSR UTWR AZBR ABOR AZPW RMPANG UTAH UTWR WYSR 0.5 j ihclrrm niaigtemgiueo eeflw (a) flow. gene of magnitude the indicating ramp color with eeto rvnItorsinin Introgression Driven Selection 0.0 0.0 10 s.e. weight Migration 10 s.e. weight Migration 0 1 0 0.5 CPL DELTOIDES WTR TIM SKN TUR MMT OFR UMI SSR RAD RMP CYH MSG JKH 0.1 0.2 THIRTEEN SKYKOMISH NOOKSACK THIRTY_ONE OLYMPIC SKAGIT PUYALLUP NISQUALLY (d) 10Migration Routes DELTOIDES (b) 8Migration Routes Drift parameter Drift parameter Drift 0.2 0.4 AZBR AZPW THIRTEEN SKYKOMISH PUYALLUP NOOKSACK THIRTY_ONE SKAGIT OLYMPIC NISQUALLY JKH MSG SSR OFR TUR SKN CYH TIM CPL MMT WTR UMI RAD RMP 0.3 0.6 ABOR Populus UTAH RMPANG UTWR WYSR Var. Expl:99% Var. Expl:99% AZBR ABOR AZPW UTAH RMPANG UTWR WYSR 0.4 0.8 balsamifera 4 Figure This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. AcceptedInterspecific HeterozygosityArticle CHHATRE 0.0 0.2 0.4 0.6 0.8 1.0 ragepo fitrpcfi eeoyoiybetween heterozygosity interspecific of plot Triangle hbi ne 1) = index (hybrid 0.0 tal et 0.2 H y b r i d

I n d e x

( F 0.4 r a c t i o n

P ● .

b ● a l s a 0.6 m .angustifolia P. i f e r a

A n c e s t r y 0.8 ) hbi ne )and 0) = index (hybrid Hybrid ZonePopsHybrid ● SSR ABOR WYSR MSG JKH RMPANG RMP CYH ● ● ● ● 1.0 ● ● ● ● ● ● ● P. Accepted Article ayn nhbi ne.Oag ein represent regions Orange ( index. genotypes hybrid in varying 5 Figure WYSR_LC117 RMPANG_07 RMPANG_01 RMPANG_05 RMPANG_08 RMPANG_10 RMPANG_06

WYSR_104 WYSR_106 Hybrid Individuals WYSR_88 WYSR_56 ABOR39 ABOR12 ABOR13 ABOR34 ABOR31 MSG_03 MSG_01 MSG_08 MSG_07 MSG_02 MSG_05 MSG_04 MSG_06 MSG_14 MSG_12 MSG_13 MSG_09 MSG_10 MSG_11 MSG_15 RMP_06 RMP_08 RMP_15 RMP_07 RMP_04 RMP_02 RMP_05 RMP_13 RMP_10 RMP_11 RMP_03 RMP_01 RMP_12 RMP_09 DMT_01 DMT_02 CYH_13 CYH_12 CYH_11 CYH_10 CYH_15 SSR_05 SSR_03 SSR_15 SSR_04 SSR_16 SSR_17 SSR_02 SSR_01 SSR_06 SSR_14 SSR_13 SSR_07 SSR_08 SSR_10 SSR_11 SSR_12 JKH_11 JKH_08 JKH_10 JKH_07 JKH_12 JKH_05 JKH_06 JKH_13 JKH_15 JKH_14 JKH_03 JKH_09 JKH_02 JKH_01 CYH_7 CYH_8 CYH_6 CYH_9 CYH_1 CYH_2 CYH_5 CYH_3 netypo hwn rbblt fseisseicgntpcacsr o h 9ppa hoooe cosarneo individuals of range a across chromosomes poplar 19 the for ancestry genotypic species-specific of probability showing plot Ancestry aa n lerpeet neseichtrzgts( heterozygotes interspecific represents blue and ) 1 This article is protected by copyright. All rights reserved. This article is protected rights by All copyright. reserved. 2 3 4 5 .angustifolia P. 6 Chromosomes Aa 7 ). 8 lk eoye ( genotypes -like 9 10 11 AA 12 ,drgenrgosrepresent regions darkgreen ), 13 14 15 16 17 18 19 0.0 P. balsamifera Ancestry .balsamifera P. Proportion 0.5 1.0

-like

eeto rvnItorsinin Introgression Driven Selection Populus Accepted Article o dpieitorsini l otta us b est itiuinof distribution Density (b) runs. bootstrap all (orange) in introgression adaptive for 6 Figure Significantly Introgressed Loci 1000 1500 2000 500 0 vs (a) ReproducibilityofIntrogressResults a erdcblt fITORS eut ae n10bosrprsmls rnebrdpcslc htwr candidates were that loci depicts bar Orange resamples. bootstrap 100 on based results INTROGRESS of Reproducibility (a) 92nua oi(gray). loci neural 1912 0 This article is protected by copyright. All rights reserved. This article is protected rights by All copyright. reserved. 25 Num. IntrogressReplicates 50 Always Sig.(1764 SNPs) Never Sig.(1912SNPs) Variably Sig.(3847SNPs) 75 100

Density (loci) 5 0 1 2 3 4 (b) F 0.00 ST

F in S T

.angustifolia P. in

P. angustifolia 0.25 Admixutre Zone eie lee rm16 addt loci candidate 1764 from alleles derived

derived alleles 0.50

F S T 0.75 Neutral (1912SNPs) Significant (1764SNPs)

1.00

tal et CHHATRE oosrflc rae nqeeso ie Otr ntesmlrt arx.Crl iei proportional is introgression. size differential showing Circle SNPs matrix). of similarity enrichment the functional in for term test the GO given of value a (warmer -log10P terms of similar the uniqueness semantically to clustering greater on a based reflect terms redundant colors minimally show Points outliers. sion 7 Figure This article is protected by copyright. All rights reserved. This article isprotected rights by All copyright. reserved. semantic space x

Accepted −5 Article 0 5 protein disulfideoxidoreductase activity EIOmlidmninlsaigpo fGn nooy(O em nihdaogintrogres- among enriched terms (GO) Ontology Gene of plot scaling multi-dimensional REVIGO potassium ion transmembrane transporter activity potassium iontransmembrane transporter serine−type endopeptidaseinhibitoractivity serine−type −5 magnesium ionbinding single−stranded DNAbinding semantic spacey ATP−dependent DNAhelicaseactivity 0 terpene synthaseactivity terpene protein kinasebinding heme binding eeto rvnItorsinin Introgression Driven Selection transporter activity transporter xyloglucan:xyloglucosyl transferase activity 5 Populus log10P uniqueness 0.80 0.85 0.90 0.95 5 4 3 2