Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ne Skrede Inger fungus rot dry the invasive of two populations in revealed histories demographic Contrasting Martin Kohler Annegret n r eonzda rwn het ofo euiy osraino idvriyadgoa economy global and biodiversity of conservation areas security, trade, new food and colonizing to practices are agriculture threats species modern growing fungal from as of (Rosenblum benefited recognized number have increasing are fungi an pathogenic and plant change Numerous climate and worldwide. globalization to Due environment, built involvedINTRODUCTION environment. the genes local to in their preadapted and to were Japan adapted populations in independently fungal substrates two and various selective These recently These of Further, more Europe. decay substrates. have environment. in to but large human-made modification related decay protein the possibly effectively and in genes replication to in establish DNA ability changes independently its rapid to functions identified to with populations analyses genes important both sweep in populations possibly appeared enabled Japanese differentiation transport, have low and intracellular may that European and revealed functions between analyses growth admixture Genomic of of corresponding Zealand. to evidence likely New related Moreover, from bottleneck, isolate tight environment. an a built in through the shown went was colonized human population it from predating probably isolates European time ago, that the the generations revealed 19,000 ago, to we - generations isolates, 3,000 split sequenced 250 populations genome Approximately these full that influence. 36 and divergent of highly analyses are genomic Japan and population species Europe using of By buildings. number including regions. environments, considerable temperate human-made fungus a in rot of advantage dry to the taken leading is have species organisms world such Many the One areas. around geographic organisms new impacted in have establishing trade international and Globalization Abstract 2021 18, February 9 8 7 6 5 4 3 2 1 pedrpdy(tknrc coad20;Col&MDnl 2017). McDonald & Croll and and 2008; colonize McDonald histories can & pathogens demographic (Stukenbrock fungal varying well-adapted rapidly where spread events, monocultures large-scale back-dispersal Gladieux involve 2010; practices and Kirk, agricultural dispersal & multiple (Brasier events to hybridization due structure genetic nvriyi Oslo in University Lorrain INRA-Universit´e de UMR1136 INRA, lantbruksuniversitet Sveriges Swansea of University Agronomique Mycea Recherche Societe la de National Lebenswissenschaften Institut fur Fakultat Agronomique Wien Recherche Universitat la de National Institut Oslo of University 8 n H˚avard and Kauserud , tal. et 1 lueMurat Claude , 00 Fisher 2010; 4 oiiu Barry-Etienne Dominique , tal. et epl lacrymans Serpula 2 auln Hess Jaqueline , 9 02 Islam 2012; hc stems grsiewo-ea ugsi norenvironments indoor in fungus wood-decay aggressive most the is which , tal. et 5 1 tal et a Eastwood Dan , epl lacrymans Serpula 3 ud Maurice sundy , 06.Teefniotnso ope population complex show often fungi These 2016). 08 04 Stukenbrock 2014; 2018, . 6 isH¨ogberg Nils , 1 ønHni Sønstebø Henrik Jørn , tal et 7 07.Modern 2007). . Francis , 1 , Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. uoenadJpns ouain r oal dpe otebitevrnet n hte rwhand the growth whether whether test We and to environment, aimed built we isolates. the Finally, Japanese to event. that adapted admixture and locally indidcated recent European are a analyses populations to between Previous due Japanese genotypes haplotypes is and of this admixed European inference. number whether demographic possessed the investigate and to using Zealand environment aimed populations New built two the from in these isolates establishment of of since populations each time divergent the two founding estimate of presence to the aimed We confirmed substrates. we large study, of this colonization In the for important were growth and be may (Eastwood CMF fungi efficient rot al. specifically Balasundaram brown other of 2017; to evolution Schilling compared The of machinery & enzymatic (CMF). mechanism reduced reaction the decay Fenton to mediated rot linked chelator brown a effective of of extremely Isolates capacity the environment. that built Japan) suggested the versus in survival (Europe long-term mantioides populations for founder crucial lacrymans independent are S. evolutionary two characteristics independent which the their indicate between compared of could consequence strain similarities a Japanese Adaptive as a characteristics for histories. physiological breath or substrate adaptations on different and populations Based (Hess sess ability indoor strain competitive Japanese regimes. European to and a (Kauserud selective related to European novel differentiated niche Nevertheless, loci, wider of highly microsatellite colonizes. a series genetically neutral it suggested a be few that imposed a units to in resource probably appear variation large environment allelic of indoor of presence the analyses scattered to and year transition the the of genetic unknown. most is and during population by populations tions Zealand exploited which New habitat However, the indoor in (Kauserud The variation populations. Zealand the source to New contributed different from have from material isolates events mainland in genetic introduction in identified higher multiple habitat was significantly and natural populations possesses MAT the population of (Kauserud European Japanese number from population the higher European transition addition, a the separate In to a environment. compared represents diversity built the population to rot Asia (Kauserud dry Zealand Japanese New the and Australia America, of population European self-recognition The and Engh (MAT) 1996; type (Raper loci and mating MAT both of of numbers number high bottleneck limited indicates population a narrow of a Engh observations for evidence the ( Further incompatibility from vegetative event. stems founder Europe a in through established European (Kauserud the individuals of low diversity few genetic very the over that is showed all microsatellites population regions on based temperate studies genetic in population constructions Previous human-made invaded has it (Kauserud which world from the Asia, in latitude study, and/or this In Kauserud quality 1960; air 2007). (Harmsen have indoor (Schmidt fungi in losses fungus few reduction economic lacrymans rot A a substantial Serpula dry cause with habitats. the may human-made structures on of species focus wooden we dimensions Such of other dry. decomposition to is the adapt environment or fungi the degree where what buildings to colonized known less is It 08.Teegnmcaaye ugse htteslcino ee eae oitaellrtransport intracellular to related genes of selection the that suggested analyses genomic These 2018). tal. et 00;Skrede 2010b; (Balasundaram oss infiatymr ffiin oddcyo puecmae otesse species sister the to compared spruce on decay wood efficient more significantly possess skont eapiaydcmoe flresbtae ohi aueadi buildings in and nature in both substrates large of decomposer primary a be to known is tal et tal. et 2007). . tal. et tal et vic tal et tal. et .lacrymans S. vic epl lacrymans Serpula lee rsn nErpa slts(asrd20;Kauserud 2004; (Kauserud isolates European in present alleles ) 03 Maurice 2013; .lacrymans S. 01.Hwvr ti o nw hte h w norppltospos- populations indoor two the whether known not is it However, 2021). . 08 Hess 2018; . tal. et 02.I a aua itiuini oie odad nhg altitude high in woodlands conifer in distribution natural a has It 2012). tal. et lee (Engh alleles 00;Coelho 2010b; vic 08,icuigissse species sister its including 2018), lee r xetddet rqec-eedn eeto cigon acting selection frequency-dependent to due expected are alleles 07 Engh 2007; a otlkl ipre i ua etr oNrhadSouth and North to vectors human via dispersed likely most has tal et tal. et eebe t aua aia ntrso eaieydycondi- dry relatively of terms in habitat natural its resembles tal. et tal. et Sruaee oeae,Aaioyee,Basidiomycota). Agaricomycetes, Boletales, (Serpulaceae, tal. et 04.Osraino aua grcmct populations Agaricomycete natural of Observation 2014). 01.Frhr eoi nlsso hs he isolates three these of analyses genomic Further, 2021). . 2 tal. et 00) vdneo ditr ewe sa and Asian between admixture of Evidence 2010b). 2017). 07.Pplto eei nlssidct that indicate analyses genetic Population 2007). tal et tal. et 00;Maurice 2010b; 07.Rcn eeepeso analyses expression gene Recent 2007). . 07,as aietdi h rsneof presence the in manifested also 2007), .lacrymans S. .lacrymans S. .himantioides S. tal. et tal et 04,sgetn hta that suggesting 2014), nErp n Japan. and Europe in a u oincreased to due was 07,suggesting 2007), . tal. et (Balasundaram 01 Presley 2011; tal. et S 2006; . hi- et Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. e sn Etos(una al21) obnddt e sn nySP aldb ohpipelines both by called SNPs only using set data combined A 2010). Hall & (Quinlan monokaryotic BEDtools the using to set mapped (Flutre were v.2.5 (Sipos call package data REPET in BCFtools the sequence using using the annotated variants were pipelines, called genome both SAMtools, For using lacrymans view. filtered Serpula BCFtools 2013), with (Li filtered BWAmem GenotypeGV- and using reads with the file (QD mapped variant VariantFiltration common cal- with a were wera Variants filtered into duplicates. combined quality PCR remove 12.5 HaplotypeCaller, further to using and once alignment (Li only CFs and each SAMtools concordantly and for using mapped Salzberg), data led & that the trimmed (Langmead reads pipeline Bowtie2 only first using the include (1) aligned pipelines: 0.3.3, two using version parallel TrimGalore in analyzed Sweden). Kit. were (Uppsala, sequences Prep Genomic Platform Technology Sample at calling SNP&SEQ bp) variant v4 108 USA) the and x at CA, SBS (2 alignment GAII Diego, SL265 using Sequence Illumina and San libraries SL198 the Inc., SL200, on bp) (Illumina, isolates sequenced platform the 125 were For 2500 France). x libraries (Toulouse, HiSeq facility (2 Illumina sequencing paired-end GeT-PlaGe the the using construct sequenced Payen to were in used Libraries described was as DNA protocol tip the Genomic genomic using without Qiagen extracted – the were CTAB 37 following SL265 a at processed Balasundaram and using min and to SL198 90 columns according SL200, Genomic-tip for samples protocol, to incubated three Genomic-tip transferred and The mix added, protocol. the 500 was Genomic-tip and in (Invitrogen) Qiagen dissolved added, then were was A was buffer samples RNase DNA QBT The mg The Qiagen RT. 2 added. on at isopropanol pooled, min min was V five were 5 phase for 0.6 samples 4 another dried aqueous and at for and The centrifugation tube EtOH centrifuged before clean 70% min. were for min a mL samples 15 30 incubated to for the for transferred and ice mixing, G was on mixed After phase 6000 incubated were aqueous at chloroform. they The centrifuged of mL G. before were 50 (V) 6000 sample, samples four volume into each The equal distributed to to was temperature. fresh added sample added room the mg was at before phenol:chloroform 500 min mortar 7:3 the 90 about mL to added Briefly, 15 was SDS) tubes. 0.5% Germany). EDTA, mM (Eastwood Hilden, 25 (see NaCl, medium (Qiagen, N Dox protocol Capex liquid Serpula from tip in on DNA grown Genomic isolates genomic Qiagen from of mycelium, the (Isolation com- using with webpage extracted JGI was bined http://jgi.doe.gov/collaborate-with-jgi/pmo-overview/protocols-sample-preparation-information/) isolates the European non-French at the available : and Zealand, protocol New phenol-chloroform and Japan a from Technology, isolates of the University of DNA Kochi Horisawa, procedures Sakae sequencing (France, and provided Dr. extraction kindly Europe and M2 were DNA France from and isolates Brest, M1 16 Japanese of isolates and Japan, University France French Floch, from respectively. Southern building. Le Japan, 18 same 1). G. the analyses, (Table of Dr. Zealand the parts by New in different from from included 2 collected were and were isolates UK) dikaryotic Poland, Norway, 36 Germany, of total A as isolates included some Isolates of ability decay wood METHODS populations. differentiation the AND the of investigated MATERIAL across islands also differences We genomic fitness for selection. of searched of measure we signals Thus, a as adaptation. sweeps local selective during and important are decay wood || tal. et ReadPosRankSum tal. et 03.()Tescn ieietimdtesqecsuigTimmtc(Bolger Trimmomatic using sequences the trimmed pipeline second The (2) 2013). 2 n rudt odri otr it Letato ue 02MTi H85 .5M 0.25 8.5, pH Tris M (0.2 buffer extraction mL Sixty mortar. a in powder to ground and 07.Rgosanttda rnpsbeeeetdrvdwr lee rmteSPdata SNP the from filtered were element-derived transposable as annotated Regions 2017). slt 73 eso (Eastwood 2 version S7.3, isolate < 80 nGnm nlssTo i GT)(McKenna (GATK) Kit Tool Analysis Genome in -8.0) tal et tal. et ° 3 t60 o 5mn h eltwswse ih20 with washed was pellet The min. 15 for G 6000 at C 21) N fteFec sltswsextracted was isolates French the of DNA (2018). . 01.Rpttv ein fthe of regions Repetitive 2011). < tal. et 2.0 || tal et 01,floigtepoeueoutlined procedure the following 2011), FS > 60.0 (2015). . || tal. et MQ μ fmliQH milli-Q of L tal. et < 01) a ahfrozen flash was 2011)), 40.0 || 00 a e Au- der Van 2010; .lacrymans S. MQRankSum tal. et ° Phytophthora .EgtmL Eight C. 2 tal. et .Tefour The O. 09 to 2009) 2014), < .2 v. - Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ditr nNwZaadisolates Zealand New analyses. in the Admixture on rates mutation of effect the tal. et higher phyla, 10 fungal x 1.98 other 10 x Regarding 10 7.29 x population. e.g. 2.4 flexible estimated, and been have reproductive basidiomycetes. rates sexually mutations decay a wood of for representative rates not mutation fungus of 10 decay rates estimates fungal of mutation wood available a of rate in from few scales mutations mutation different reaction also somatic a the all a are Recently, explaining taxa, to generation, There other next lead to the organisms. will Compared to across habitat contribute fungus. will to human-made the chance frequency of the a death fruiting have in the individual the fruiting often that and conditions owner plausible sub-optimal home probably highly the and under is year, Alternatively, one It after years. extensively. fruit vary and The several quickly for extremely analyses. expand such successively and for grow fruit used colonize, commonly can as fungus the calculated, conditions, was used years for approach than time rather analyzed. bootstrap generations generation were parametric of the cycles number The using 40 the calculated year. and to were simulations fitted estimates Excoffier coalescence (SFS) point each in 1000000 For spectrum the Fastsimcoal2. of frequency for in intervals runs site calculated population. 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Japan, for highly was current and be population Europe understanding to the between for when shown divergence the been important diverged to has is that addition population populations size In where natural two houses. population scenario from into a in Europe, colonization represents and the Japan model to in second prior independently model The environment, first built The Europe. the into literature. in of the environment from divergence evolutionary built known the of the is where test timing what To scenario, by as a supported well models. represents evolutionary models, as demographic evolutionary different rate, addition, realistic the growth three In for population defined estimated compared. size, be population be Excoffier can effective can events, 2011; the models Foll as evolutionary & such predefined parameters, (Excoffier of Fastsimcoal2 likelihood in the implemented Fastsimcoal2 of approach history produced demographic model-based were the axes infer the to PC used Three were the simulations analyses. analyses. in Furthermore, Coalescent Admixture PCA analyzed the three in plot VCFtools. the as PCA of isolates) in a each Japanese format by for the (Danecek and visualized plink VCFtools (European were in to sets populations 1 data format within [?] vcf and (Price count The between from European allele Eigensoft K. distance only transformed absolute minor of genetic were the by sets and determine data reduced datasets variation reduced to set to All try data addition not in (SNP does analyzed, 2011)). error isolates but were CV accuracy, Japanese SNPs The predictive and only K. isolates best and each all the for including has in set error K implemented data (CV) which full cross-validation as find the approach to and clustering used (K) model-based is populations of a number used different we analyzing dataset, the (Alexander of Admixture structure analysis. the this investigate in To included history isolates demographic 36 and the structure for Population SNPs quality high 419,196 in resulted 08.Tu,uigbt uainrtso 10 of rates mutation both using Thus, 2018). -6 -8 o26x10 x 2.6 to in tal et anprh oryzae Magnaporthe 21) eaaye h aawt oh10 both with data the analyzed We (2013). . tal. et rilragallica Armillaria .lacrymans S. -6 tal. et 06.TePAaaye eerno h ulSPdt e,adas ntesplit the on also and set, data SNP full the on run were analyses PCA The 2006). o soyeeyeast ascomycete for 09.FrteAmxueaaye h ubro ouain a nerdby inferred was populations of number the analyses Admixture the For 2009). .lacrymans S. -10 spoal ihycnetdpnet o ntne ne pia growth optimal under instance, For context-dependent. highly probably is Acmct)uigtpdtn ftmoal eaae ape (Gladieux samples separated temporally of dating tip using (Ascomycota) a siae o igedpodidvda ftefna ahgnand pathogen fungal the of individual diploid single a for estimated was (Anderson oe oa norevrneti aa,bfr irtn to migrating before Japan, in environment indoor an to moved acaoye cerevisiae Saccharomyces tal. et -7 -7 n 10 and o h chytrid the for 4 08.Ti eaieyso uainrt sprobably is rate mutation slow relatively This 2018). -8 nordmgahcaaye losu oexplore to us allows analyses demographic our in -7 n 10 and .lacrymans S. .dendrobatidis B. 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Data may be preliminary. ic aclto fX-H sdpneto nweg fhpoye,tedt a rtpae using phased first was data the 2012). haplotypes, Vitalis 2006). & of Stephens (Gautier & knowledge rehh (Scheet approached on program settings has R dependent default allele the with selected is using v.1.4 the XP-EHH done fastPHASE which was of in analysis sweeps calculation The selective homozygosity Since detect population. haplotype to one haplotype approach extended within integrated XP-EHH fixation population the the on using the focused population applying we within populations both (Voight between investigated (XP-EHH) or be analyzed (IHH) can were sweeps homozygosity 2011). files Excoffier selective resulting & The of (Lischer Signatures settings. 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Zealand contains between New allele relationship structure the between the using haplotype relationship identify haplotype populations the to and between However, used allele relationship be Admixture. in the may as changes of large such estimates effect in methods, strong complicate resulting in frequency-based events result often founder will disequilibrium, size Thus, linkage population increased effective frequencies. and small the drift founders, genetic initial of few a involving events founder In tal et 2 92 n uloiesbttto e ie(D site per substitution nucleotide and 1992) . ausfrec itnebtenlc eepotdi ovsaieL ea.Gvnthat Given decay. 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Data may be preliminary. 9-5) n atica2aaye niae htol i altpswr novd(ofiec interval: (confidence involved were interval haplotypes (confidence six ago generations only models, 250 that two about the indicated bottleneck between analyses only strong likelihood Fastsimcoal2 with a in and scenario through the difference 198-650), went than (the likely population Europe more European was in The size change population size in population change a a 18,770 to experienced increased population 10 which Japanese of estimated rate, the mutation rate The selected mutation the 4). a to Figure sensitive with highly 2012-6157; generations was interval generations) rate (confidence mutation (i.e. ago a time generations 7, divergence on 3,000 southern = based These around analyses K a Demographic groups. population into southern Japanese and 2). population three (Figure European France, Japanese and PCA the the the groups eastern 10 splitting in admixed of 4, in recognized When additional partially = three groups 2). also identified, were K (Figure two was groups For plot group group, PCA northern revealed the European 2). distinct separately in a and northern visible populations 1 a also Japanese (Figure group, into admixture French and the populations divided European in both was the population within population on European sub-structuring the performed geographic from analyses further and from PCA Japanese plot separated separated and the was 1d). 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(Table S7.3 ST n D and XY siae ofimdta the that confirmed estimates .lacrymans S. Δ ST I 58,899). = AIC tal et f052 D 0.572, of (2018). . Abies were XY Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. aaeepplto eosrtdamr ai Ddcy(iue6.TeErpa ouainpossessed population European The 6). the ( (Figure while ( decay diversity decay, LD LD genetic dis- slow rapid lower linkage with more of a disequilibrium, a levels linkage their demonstrated strong in population possessed populations Japanese population Japanese and European European The the equilibria. between differences marked were There throughout European scattered the regions population. with smaller Japanese other ancestry diversity the with Population common together with showed 3, ancestry and ICMP18202 shared 1 showed isolate scaffolds genome, whole of of the the portion along genome large isolates the a European but with of ancestry population, analyzed majority was common admixture 100% The of shared level 950 the genome. 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No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. oe eei iest,cvrtolregnmcrgoscnann aygnswt aiu ucin.One functions. various with is genes many This containing regions event(s). genomic founder large two ( its cover (Engh incompatibility diversity, during the population genetic vegetative than retained lower Japanese variable of was the more number variation in genetically higher present genetic is the natural more population by the Japanese that mirrored to the and closer that population confirmed genetically European data and SNP geographically genome-wide is The population (Kauserud Asia Japanese East the in that population and Himalayas, the oreppltoso h urn norppltosi uoeadJpn rmpeiu ouainstudies population previous distribution From natural Japan. and westernmost Europe may it in areas populations has same cold indoor the of fungus current and almost the the at of dry where size populations The Himalayas, source population in the 2016). Consequently, reduction Jiang estimated & (Kauserud the split. 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Kauserud this human 3,000 by support revealed than predated strongly previously populations analyses as two divergent, modelling the highly between are strains, of Europe divergence the populations and among two Japan rate the in decay that the confirmed in strains, We variation all 8). higher by (Figure were fastest significant decayed there not decomposition were was pine DISCUSSION conducting populations Spruce For by the among fitness Zealand. pine. differences of New then the measure and however and a Japan fir as Europe, by efficiency any from followed decay without isolates wood of one in experiments and differences assessed 79617), also ID 10 We (protein Interpro a P450 domain Within Cytochrome Interpro assessment 32. a decay WW Wood with scaffold a one on with genes, genes one predicted predicted the domains. three 79618), between conserved population, are ID locus there Japanese GDP-fucose (protein a sweep a the in scaffold domain this and For in sweep surrounding Pif1-like gene selective window a helicase 3). a kb and DNA (Table 79617) detected with respectively ID analyses annotated (protein domains, EEH 8 1), Interpro scaffold Table in O-fucosyltransferase Supplementary gene protein 77115; a ID in located (protein population, 13 European the in sweeps .lacrymans S. S . lacrymans var. tal. et .lacrymans S. lacrymans shg liergoswt ctee ag oie os(Kauserud logs conifer large scattered with regions alpine high is ti nw htteErpa ouainsae eei aeilwt pcmn from specimens with material genetic shares population European the that known is it , 02,adaohrnrhEsenAinpplto,mgthv ucinda separate as functioned have might population, Asian Eastern north another and 2012), a salse neednl tlattiei h norhbtt(Kauserud habitat indoor the in twice least at independently established has norfga hssplitting thus refugia, into ehv rvosysgetdta hsseisi n ffwwo-ea fungi wood-decay few of one is species this that suggested previously have we , epl lacrymans Serpula tal et 02 2007). 2012, . tal. et epl lacrymans Serpula 00) h w eei ein nsaod1ad3with 3 and 1 scaffold in regions genetic two The 2010a). .lacrymans S. 8 .lacrymans S. var. -8 satraiemtto ae(o10 (to rate mutation alternative as shastensis vic var. tal. et a efudi aue eentcovered not were nature, in found be can nosvrlsbppltos Although sub-populations. several into lee n iest fmtn types mating of diversity and alleles ) lacrymans tal. et 02.Hwvr ogrgeneration longer a However, 2012). n h uligoccupant building the and 08.A eut testablished it result, a As 2018). rmtebitenvironment built the from tal. et tal. et 20) n htthe that and (2007), h aua habitat natural The 02.Fo there, From 2012). -7 tal et .Assuming ). 2007). . 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Data may be preliminary. nteJpns ouain.TeSF ope sivle ngn xrsinrglto sarsos to response a environmental as different several regulation to expression responses in gene involved SNF1 Shashkova be in the to in involved shown selection i.e., (summarized also is balancing involved, is stressors but complex but and be populations, 2003), SNF1 (Sanz may D European The yeast the in Tajima’s effects starvation in these populations. pleiotropic in selection where Japanese purifying that differences phenotypes), of the indicate The signals more in show loci or 8 two populations. two scaffold two these at on complex at the effect an populations in having F the pressure lower locus between selection significantly (one different observed effects we have pleiotropic loci phenotypes by two these caused For be loci. could two (D decay. on expected linkage acting than slow selection values the environment. purifying of built or explanation balancing the main of in the selection not of is Signatures dispersal clonal mating (Kauserud or studies tetrapolar selfing previous the that available or and supporting alleles our individuals, mating in between found of opportunities were number isolates mating limited in The reduction inbreeding. of a biparental system to of levels peninsula lead high Iberian necessarily the to will and led Italy also in and probably cause disequilibrium populations has may decay linkage wolf dispersal of LD inbred clonal biparentally patterns slow or highly Similar selfing (Pilot the and of 2016). isolated in degree James for high reflected & observed A (Nieuwenhuis were also curves population. decay is European linkage the population abnormal in such European observed founder Fis the tight of establishing levels very nowhigh event through are founder continents there other small Hence, on The growth. establish 2010). may population Kirk extensive fungi & invasive by (Brasier followed that pathogenicity events evidence high of with lines hybrid multiple a produced populations these asite (McMullan individuals haploid (Kauserud two fungus diversity only dieback allelic ash entire invasive the for the account may ( only al. isolates incompatibility assumption that heterokaryotic vegetative et This possible three and is where (MAT) population. it mating population European Hence, entire few ropean the by rate). mutation founded supported on and strongly (depending colonized is haplotypes isolates heterokaryotic five three or or four two only of consist to mated of population investigated. European further The be should Himalayas the in range of event nization lychnidis-dioicae of have description easily could species al. which spread the further Asia have and with might Europe activity well between of fits activities gen- colonization trade generations the a considerable vectored Assuming 200-400 were there of ago. earlier, generations estimate somewhat 400 this and year, 200 one between lacrymans happened of popu- Europe indoor time of European eration colonization the the the and (Singh Currently, that ago. forests observed suggests in generations been this. collected previously 250 specimens test has about Himalayan lation to environment between built required similarity genome the genetic is better invaded above, unknown. However, data are population rearrangements sequence European isolate). genome read The Zealand possible rates long New these lower of with show one effect achieved therefore in and and be (and function inversions can population harbor which Japanese regions the assemblies, genomic in two recombination these of that is interpretation possible 07 n sas osdrdtemi gn o ipra fsvrlpatptoes uhas such pathogens, plant several of dispersal for agent main the considered also is and 2007) pisoanovo-ulmi Ophiostoma 06 Engh 2006; tal. et .lacrymans S. n18 Wle 71,bsdo olcinfo uoe(uti) uigti eid n also and period, this During (Austria). Europe from collection a on based 1781), (Wulfen 1781 in 04.Tevr o ubro sltsfudn h uoenpplto of population European the founding isolates of number low very The 2014). S and tal. et . lacrymans pisoaulmi Ophiostoma tl los2%o h prsfo h aefutbd omt.N uaieclonal putative No mate. to body fruit same the from spores the of 25% allows still XY 00;Skrede 2010b; a o ieetfo h xettos.Gnmcrgoso o differentiation low of regions Genomic expectations). the from different not was .lacrymans S. salse scoa aaie nErp.Ltr eulrpouto between reproduction sexual Later, Europe. in parasites clonal as established .lacrymans S. nErp,terltdeso uoenioae oioae rmtenatural the from isolates to isolates European of relatedness the Europe, in .fraxineus H. .lacrymans S. tal et tal. et Bair19;Fontaine 1991; (Brasier tal. et oErp,eg hog h rd n rnpr ftme.Human timber. of transport and trade the through e.g. Europe, to 05.Tehmlgo h anSF iaewsdifferentially was kinase SNF1 main the of homolog The 2015). . od o eei iest,adtefudn ebr eeesti- were members founding the and diversity, genetic low holds tal. et 03.Smlrto Similar 2013). 08.Todffrn useiso h uc l ies par- disease Elm Dutch the of subspecies different Two 2018). sgntclyeteeyhmgnu n a salse by established was and homogenous extremely genetically is rmErp oNrhAeiaadAsrla(Kauserud Australia and America North to Europe from , 93 Kauserud 1993; 9 nbt ouain,w bevdsgasindicative signals observed we populations, both In tal. et 07 Engh 2007; tal. et .lacrymans S. tal. et 03.T etrudrtn h colo- the understand better To 2013). 07.Ordmgahcmodelling demographic Our 2007). tal. et vic h uoenpplto of population European the , 00;Maurice 2010b; lee eetdi h Eu- the in detected alleles ) Microbotryum .lacrymans S. tal. et snoted As 2014), ST S. et π Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. h esn o eue iest n ditr nlregnmcrgosi h die slt from isolate admixed isolates. the Japanese the in of regions genomes genomic the large of rest in the admixture to and compared admixture diversity as detects diversity reduced readily lower more for with hence, windows 1 reasons and 3 genomic diversity, scaffolds The assigned and low PCAdmix (mainly 1 with that genome regions scaffolds be be the genomic also in could homogenous could in admixture It to the distributed recombination. readily admixture, of to heterogeneously more of cycles needed was signals limited are showed admixture indicating isolates isolates 3), the two more and Further, the though event. of 8), recent one (Figure only a rapidly Since wood pattern. pine this decayed (Ioos confirm ICMP18202 species isolate these McMullan Zealand of 2010; New most Kirk & for Brasier shown 2008; as genotypes, aggressive more like fungi, (Ioos invasive al. as observed other ancestry, been et have in admixed lineages Similarly, evolved an hypothesis. independently has between this population of this support whether , in test alleles, populations. to Japanese Asian us and and enabled Kauserud Zealand European required in New between therefore hypothesized from admixed are isolates is studies two functional population that of detailed European P450s. rather Zealand in More cytochrome the populations, New trait. differences individual European from The of this systematic the functions isolate in detect and the variation an not understand Japanese strain did to better to the we to compared strain between study significantly high substrates isolate current is different with Japanese the there decay associated a in to was in ability experiments P450s the the wood cytochrome in pine expressed However, recalcitrant differentially population. of of two for repertoire decay found larger faster been a previously have 2021), P450s (Wymelenberg . cytochrome of species expression decay gene wood in in difference tolerance dependent metal type between heavy Wood interactions in encountered pathogenic Xu involved genes, or involved during 2013; be predicted organisms be and Ichinose to three other to 2011; by suggested are known Petric secreted recently there enzymes and molecules were sweep monooxygenase (Cresnar defense this decay are other of P450s and wood window polyphenols Cytochrome during about of P450. kb conclude detoxification Cytochrome 10 cannot the we a a in Thus, is within region. one However, non-coding which sweep. the a of this in and founded was of size population recently function population Japanese the effective for the in small adaptation well sweep its selective corresponds local with The which population, of events, recent European signals observing the first be bottleneck. of may recent the history we demographic be population the European may with the replication in Thus, DNA populations. studies, of genomic modification landscape that several this, in to found parallel fungus been brevipes In decay have glycosylation). wood environment in helicase involved the the DNA domain i.e. (a and (O-Fuct replication helicases modification DNA between to protein related and associations genes domain) in Pif1 found were a sweeps with substrates. selective population, large European of the hyphal decay for In important and polarized be growth to therefore important rapid could complex for be SNF1 ability to the shown unique and have oxysterol-binding the and analyses) both 2019), for our Zeng diversity in & in growth Qui 27 and in scaffold formation (revised at cells eukaryotic locus in the lipids in in dN/dS) found higher himantioides (significantly was pace S. (as rapid specifically domain a oxysterol-binding at evolved an with gene Another in decay (Hess wood regulation during gene composition substrate-dependent substrate in varying to response in expressed .um/ooum,H fraxineus H. ulmi/novo-ulmi, O. 08 O’Hanlon 2018; (Branco (Balasundaram tal. et tal. et 07 n h e ra mold bread red the and 2017) Candida hloiu nigrolimitatus Phellopilus tal et 08.Temrigo eei iegsi one ra a edt oe and novel to lead may areas founder in lineages genetic of merging The 2018). 20) ned slt CP80 osse obnto fEuropean of combination a possessed ICMP18202 isolate Indeed, (2007). . tal. et and tal et n h oyeepathogen oomycete the and tal. et Aspergillus 08.Oytrlbnigpoen r novdi rnprainof transportation in involved are proteins Oxysterol-binding 2018). 01.Frhr norrcn td of study recent our in Further, 2011). . 08 O’Hanlon 2018; eeoaiinannum Heterobasidion tal et (Ghugtyal 2021). . 10 (Sønstebø ersoacrassa Neurospora tal. et tal et tal et tal et tal. et htptoaalni Phytophthora .lacrymans S. 08.I u oddcyeprmn,the experiment, decay wood our In 2018). 05 B 2015; . n oie re (Karlsson trees conifer and ulu luteus Suillus npe.,teectomycorrhizal the prep.), in . tal. et 06 rse ik21;McMullan 2010; Kirk & Brasier 2006; 05.Frfni yohoeP450s cytochrome fungi, For 2015). . (Ellison 06 tknrc McDonald & Stukenbrock 2006; uhler ¨ .lacrymans, S. oprdt h itrtaxon sister the to compared tal et (Bazzicalupo .lacrymans S. tal et eodr admixture secondary , 05.Maintaining 2015). . 01.Suggesting 2011). . uprigarole a supporting .dendrobatidis B. .lacrymans’ S. tal. et tal. et (Hess Inclusion Suillus 2008). 2019) tal et Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. r-dpe blt oivd buildings. invade MB to Durling ability J, pre-adapted Hess SV, Balasundaram D individual. Kasimer fungal JN, Bruhn JB, Anderson individuals. unrelated All in ancestry of manuscript. estimation model-based Research Fast the (2009) Genome K wrote Lange J, and Novembre DH, results Alexander from DB-E interpreted manuscript. DNA SM, the HK extracted IS, of and and version data. final cultured DE REFERENCES analyzed the IS and JHS, approved sequencing study. and SM, organized commented the JH, JHS read, designed and IS, authors HK AK and JH, samples. FMM CM, contributed DE, IS, NH, samples. non-French JHS, all SM, JH, CM, IS, interests. competing CONTRIBUTIONS no AUTHOR have they that declare authors The (ANR-11- ARBRE University. INTEREST Forest Excellence Beijing OF of Innovation Design, CONFLICT Advanced Laboratory Molecular Beijing Life by the and and for Breeding Fund Knut by Tree Science Development the funded for Regional and and Center the is Council European Sweden along Research lab Lorraine, (NGI) Swedish pi Region FMM’s Infrastructure the LABX-0002-01), in and by Genomics Platform Foundation. Dxy supported Technology National Wallenberg also Fst, SNP&SEQ the acknowledge is Alice for the Platform We of by scripts SNP&SEQ part performed The his funding. is was Laboratory. of for facility SL265 use and The 254746) the SL198 (project Uppsala. allowing SL200, Norway JHS, of for SM, of Sequencing Cambridge, and Council genome. 221840) of Research (project University Norway the Martin, of acknowledge Council Simon of Research HK isolates and plan- and for Oslo tree of University) IS University Christmas (Aberystwyth the Skui acknowledge Griffith help, HK Gareth technical JH, and for Technology) Sacre of Alexandre University and the Thoen for Ella tation Thorbek, Lisbeth thank We nee- environment. are built signatures of populations the genomic populations ACKNOWLEDGEMENTS Asian in source held native populations the Zealand the the certainty New and of better history Zealand from influence evolutionary with New isolate Europe from infer, one in samples to that modification more ded protein confirm However, and ancestry. to replication admixed able various DNA of environment. were of of We built decay adaptation that survival. the show rapid in of population which invasive and survival events, became Japan recent a for more in species through important identified the substrates sweeps ago particularly before selective generations seemed 19,000 evolved specific 400 growth to probably population mycelial – However, 3,000 and 200 to population populations related about Japanese indoor genes established the both Two population from event. European split bottleneck the population tight that European and the ago, of generations population source of the isolates that among differences genomic geographic full the remarks. population Japanese from Concluding isolates on of more necessarily effect including Thus, not their Asia. synteny, were on in of admixture genomic locations light other distribution the shed of from to recombination, originate may analyses could contributed low populations but that thorough of origin, three isolate(s) areas more these the genomic future, Furthermore, among of divergence. genomes, the consequence assembled In a on rearrangements. be based could chromosomal This from unknown. resulting currently are Zealand New be lasiocarpa Abies .lacrymans S. rceig fteRylSceyB ilgclSciences Biological B: Society Royal the of Proceedings , 19 1655–1664. , yuigfl eoedt ncmiainwt rwheprmns erevealed we experiments, growth with combination in data genome full using By a otiuet etrudrtn h ditr vn nNwZealand. New in event admixture the understand better to contribute may odadD.Gea eFoh(nvried rs) aa oiaa(Kochi Horisawa Sakae Brest), de (Universite Floch Le Gaetan Dr. and wood tal. et .lacrymans S. h SEJournal ISME The tal. et 21)Coa vlto n eoesaiiyi 2500-year-old a in stability genome and evolution Clonal (2018) 21)Tefnu htcm nfo h od r rot’s Dry cold: the from in came that fungus The (2018) 11 rmErp,JpnadNwZaad eestimated We Zealand. New and Japan Europe, from , .lacrymans S. 12 791–801. , , 285 n o ndphaaye fthe of analyses in-depth for and 20182233. , .lacrymans S. IS, . Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. lmnosfungus filamentous nhI,Srd ,Ser -,Kueu 21b ihvraiiyi aigtp ikdrgo nthe in region linked type mating a in variability High (2010b) H Kauserud fungus G-P, rot Saetre dry I, Skrede IB, Engh G-P Saetre T, lacrymans Carlsen IB, Engh eukaryote. D microbial Kowbel model C, Hall CE, Ellison fungi. forest of M diversity Binder functional D, Floudas agricultural DC, in Eastwood fungi pathogenic for G 2156–2158. adaptation Abecasis , A, local Auton of P, basis Danecek genetic The (2017) BA ecosystems. McDonald kingdom. fungal D, the Croll in enzymes P450 Proteomics Cytochrome and (2011) Protein Basidiomycota. S Acta, The Petric Sex: and Fungal B (2017) Cresnar T Giraud ME, Hood S, Sun Spectrum G, for Bakkeren inference MA, missing-data Coelho and clustering. phasing haplotype haplotype localized accurate of Genetics use and by Rapid studies (2007) association whole-genome BL Browning populations. SR, more or Browning two from ancestry admixed with individuals , in J chromosome of Byrnes each along subspecies K, two Bryc the A, between Brisbin hybrids of emergence Rapid (2010) ulmi SA Kirk CM, Brasier Mycopathologia (1991) CM Brasier P mushroom Gladieux the in H-L, adaptation Liao ronmental K, Bi S, Branco data. sequence Illumina for trimmer B flexible a Trimmomatic: (2014) B Usadel formatics M, Lohse variation. AM, number Bolger copy and allelic through tolerance Y-H metal Ke J, Ruytinx AL, Bazzicalupo xoe n olM(01 atica:Acniuu-iecaecn iuao fgnmcdvriyunder diversity genomic of simulator coalescent scenarios. continuous-time evolutionary A complex fastsimcoal: (2011) arbitrarily M Foll and L Excoffier lteT urtE eiltC useil 21)Cnieigtasoal lmn iesfiainin diversification element transposable Considering (2011) H Quesneville C, Feuillet novo E, Duprat T, Flutre CJ from Briggs inference DA, health. demographic Henk Robust MC, (2013) Fisher M Foll VC, data. Sousa SNP E, and Huerta-Sanchez genomic I, Dupanloup L, Excoffier 84 he ,Hgwr ,TksiaN(05 ucinlaayi fseo rnpre rhlge nthe in orthologues transporter sterol of analysis Functional (2015) N Takeshita D, Hagiwara N, uhler ¨ 343–364. , ihahg ee fptoei fitness. pathogenic of level high a with noainapproaches. annotation Nature , , , 81 hwdvretpplto eei structures. genetic population divergent show 5 30 oeua Ecology Molecular 1–23. , 1084–1097. , 2114–2120. , epl lacrymans Serpula , , 484 115 piitm novo-ulmi Ophioistoma seglu nidulans Aspergillus 186–194. , 151–161. , lSGenetics PloS rceig fteNtoa cdm fSine fteUSA S U the of Sciences of Academy National the of Proceedings LSONE PLOS tal. et , tal et 1814 , 26 asdb rqec-eedn selection? frequency-dependent by caused tal. et tal. et tal. et 2027–2040. , Science 21)Pplto eoisadlclaatto nwl sltso a of isolates wild in adaptation local and genomics Population (2011) . 21)PAmx rnia opnnsbsdasgmn fancestry of assignment components-based principal PCAdmix: (2012) tal et 29–35. , tal. et , tal et ulu brevipes Suillus . 21)Tevratcl omtadVCFtools. and format call variant The (2011) 9 21a w naieppltoso h r o fungus rot dry the of populations invasive Two (2010a) uayt Cell Eukaryote 21)Icpetlclaatto nafnu:eouino heavy of evolution fungus: a in adaptation local Incipient (2019) . 21)Eegn ugltrast nml ln n ecosystem and plant animal, to threats fungal Emerging (2012) , p o. astv gn fcretDthemdsaepandemics. disease elm Dutch current of agent causative Nov., sp. . 21)Tepatcl aldcmoigmcieyudristhe underlies machinery wall-decomposing cell plant The (2011) Bioinformatics , 6 ln Pathology Plant 21)Cnietllvlpplto ieetainadenvi- and differentiation population Continental-level (2017) . 333 e16526. , 762–765. , 12 . oeua Ecology Molecular , oeua Ecology Molecular 14 , bioRxiv 27 , 908–921. , 59 1332–1334. , 186–199. , doi.org/10.1101/832089. , h mrcnJunlo Human of Journal American The M Genetics BMC , , 19 26 706–715. , 2063–2076. , iciiae Biophysica et Biochimica Bioinformatics pisoanovo- Ophiostoma , 108 , ua Biology Human 11 Microbiology 2831–2836. , 64. , Serpula Bioin- , 27 de Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. esJ aaudrmS,BkeoRI Bakkemo SV, Balasundaram J, Hess iH(03 lgigsqec ed,coesqecsadasml otg ihBWA-MEM. with contigs assembly and sequences clone reads, sequence 2. Aligning arXiv:1303.3997. Bowtie (2013) with alignment H gapped-read Li Fast (2012) SL Salzberg B, Langmead recognition fungus self/nonself G-P rot of Saetre dry Genetics IB, Svegarden (2006) H, T Kauserud Schumacher C, Decock O, Schmidt popula- in G-P, and Saetre dispersal, H, worldwide fungus origin, Kauserud rot Evolutionary dry (2012) the I of Skrede N, genetics Hogberg tion H, fungus Knudsen H, dry-rot Kauserud the the during in groups expressed compatibility is vegetative Mycologia P450 Widespread (2004) cytochrome H fungal Kauserud A (2008) A Olson , J, pathogen fungal Stenlid the between M, interaction Elfstrand M, Karlsson of lineage P American Gladieux species D, hybrid Croll natural MT, the Islam of characterization Genetic (2006) 511–529. P , applications. Frey biotechnological B, alni Marcais and tophthora A, basidiomycetes Andrieux R, wood-rotting Ioos of P450 Biochemistry Applied Cytochrome and subdivision. Biotechnology (2013) geographic detecting H for test Ichinose statistical A (1992) Evolution NL and Kaplan Biology DD, Boos RR, Hudson fungus invasive the in genus machinery the of species spored brown on studies cultural and , Taxonomic (1960) L Harmsen pathogen. A blast Rieux rice S, Ravel P, Gladieux eukaryotes. in divergence H, adaptive Badouin of mechanisms J, Ropars A P, S Gladieux U the of growth. Sciences Phosphatidylinositol- data filamentous (2015) of fungal RA SNP Academy for Arkowitz genome-wide critical M, is Bassilana in traffic S, selection membrane Schaub 4-phosphate-dependent A, of Seminara footprints R, detect Garcia-Rodas V, to Ghugtyal package R an structure. rehh: haplotype (2012) from R Vitalis M, Gautier pathogen smut anther T the yeasts. Prahl of J, invasion Steensels the B, of Gallone History (2013) dominant T both Giraud for ME, appropriate on Hood P, loci Gladieux selected MC, identify Fontaine perspective. to Bayesian method a genome-scan markers: A codominant (2008) and O Gaggiotti M, Foll 19 6 epl lacrymans Serpula ieelatifolia Silene 233–277. , 115–120. , Cell , 96 , 166 sifre rmnceradmtcodilDAanalyses. DNA mitochondrial and nuclear from inferred as epl lacrymans Serpula 232–239. , 1397–1410.e16. , nNrhAmerica. North in mBio anprh oryzae Magnaporthe . uglGntc n Biology and Genetics Fungal , 9 138-151. , Bioinformatics , 9 e01806–17. , tal. et tal. et tal. et epl lacrymans Serpula epl lacrymans Serpula . , oeua Ecology Molecular tal et 112 21)Ceitneo utpeedmcadpnei iegso the of lineages pandemic and endemic multiple of Coexistence (2018) 21)Eegneo ha ls nBnlds a asdb South a by caused was Bangladesh in blast wheat of Emergence (2016) 21)Dmsiainaddvrec of divergence and Domestication (2016) h e Phytologist New The eeoaiinansmsnulato sensu annosum Heterobasidion tal. et tal et . , 8644. , , 21)Fna vltoaygnmc rvdsisgtit the into insight provides genomics evolutionary Fungal (2014) . 60 M Biology BMC 28 22)Ncedffrnito n vlto ftewo decay wood the of evolution and differentiation Niche (2021) . 20)Ainoii n ai lblsra ftedestructive the of spread global rapid and origin Asian (2007) 71–81. , 1176–1177. , oeua Ecology Molecular Genetics , 13 . 43 . h SEJournal ISME The , uglBooyReviews Biology Fungal 16 , 503–510. , 14 , 3350–3360. , , 198 84. , 180 946–956. , 977–993. , , 23 uglGntc n Biology and Genetics Fungal 753-773. , , n oie trees. conifer and 15 aueMethods Nature acaoye cerevisiae Saccharomyces 592–604. , , rceig fteNational the of Proceedings 26 84–93. , epl lacrymans Serpula Merulius N Sequence DNA , 9 357–359. , BioRxiv Molecular . Friesia Phy- beer , 43 , . Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hskv ,Wlehye ,HhanS(05 oeua omncto:cosakbtenSf and Snf1 between crosstalk communication: Molecular (2015) pathways. S signaling Hohmann other and N, identification Welkenhuysen physiology, S, fungi, Shashkova causal damage, control. basidiomycetes: and prevention wood-decay characterization, Indoor (2007) O data: Schmidt yeast. type genom phase. in population haplotypic large-scale stress and for cellular genotypes model 78 statistical to missing flexible inferring response and to fast the A applications in (2006) M player Stephens P, key Scheet a emerging kinase: an of protein Transactions story Snf1 Society a (2003) fungus: P chytrid deadly Sanz The (2010) Ed,). JE Madhani, Stajich (HD TJ, pathogen Poorten J, Voyles EB, features. Rosenblum genomic comparing for (1996) utilities JR of Raper suite flexible a and BEDTools: yeast (2010) in formatics IM homologous Hall protein oxysterol-binding AR, the Quinlan of understanding in Advances fungi. (2019) filamentous B Zeng S, Qui studies. divergent association RM genome-wide taxonomically Plenge in two NJ, for Patterson strategies AL, secretome Price and growth Distinct fungi. (2017) rot brown JS Schilling GN, Presley BM wolves. Holdt European von in selection C, diversifying Greco M, Pilot ( truffle black Perigord the Resources A in Gigant resequencing genome C, through Murat T, Payen declines. RA Farrer A, fungi. Rieux SJ, in O’Hanlon sex Sciences Biological of B: frequency London The of (2016) Society TY James endonucleases. BPS, restriction Nieuwenhuis Sciences of terms of in Academy variation genetic National studying the for model of Proceedings Mathematical (1979) WH Li M, Nei individuals. G divergent Kaithakottil genetically two M, Rafiqi M, McMullan data. sequencing DNA E next-generation of Banks analyzing structure M, Population population. Hanna French (2014) A, the H McKenna to Kauserud outlook G, an Barbier with G, Europe population LeFloch in connecting I, for Skrede tool S, conversion Maurice data automated programs. an genomics PGDSpider: and (2011) genetics L Excoffier HEL, Lischer A Wysoker formatics B, Handsaker H, Li 629–644. , Science , , , 26 25 15 841–842. , 2078–2079. , 1243–1255. , ple n niomna Microbiology Environmental and Applied eeiso eult nhge fungi higher in sexuality of Genetics , 360 nentoa Microbiology International , 31 621–627. , 178–181. , ESYatResearch Yeast FEMS lSPathogens PloS tal. et tal. et Bioinformatics tal. et tal. et tal. et aueGenetics Nature tal. et aueEooy&Evolution & Ecology Nature 20)TeSqec lgmn/a omtadSAMtools. and format Alignment/Map Sequence The (2009) 21)Asre fgnm-iesnl uloiepolymorphisms nucleotide single genome-wide of survey A (2015) 21)TeGnm nlssTokt aRdc rmwr for framework MapReduce A Toolkit: Analysis Genome The (2010) 21)Rcn sa rgno hti ug asn lblamphibian global causing fungi chytrid of origin Asian Recent (2018) yooia Progress Mycological tal. et , Heredity 371 21)Gnm-iesgaue fpplto oteek and bottlenecks population of signatures Genome-wide (2014) 20)Picplcmoet nlsscret o stratification for corrects analysis components Principal (2006) , 21)Teahdeakivso fErp a one by founded was Europe of invasion dieback ash The (2018) . 22 , , 6 , , 28 eoeResearch Genome 15 169-179. , 76 e1000550. , , 14 112 298–299. , , Mycologia fov026. , 5269–5273. , oadPesCmay e York. New Company, Press Ronald . 38 428–442. , 904–909. , , ue melanosporum Tuber 83 , 6 . , 281–281. , 106 , mrcnJunlo ua Genetics Human of Journal American hlspia rnatoso h Royal the of Transactions Philosophical 2 , 20 1000–1008. , 889–895. , 1297–1303. , Vittad.). epl lacrymans Serpula oeua Ecology Molecular Biochemical Bioin- Bioin- , Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. uJ agXY u - 21)Tectcrm 40spraiy e lyr npatdevelopment plant in players Key superfamily: P450 cytochrome The (2015) W-Z defense. Guo and X-Y, Wang J, Xu Microbiology human M the Mozuch fungi in decay J, selection Gaskell positive 111. AV, 2, recent Wymelenberg austriac., of Miscell. map Jacquin, A in (1781) (2006) Wulfen JK Pritchard X, Wen data. genome. S, genomic Kudravalli in BF, selection Voight natural Detecting (2013) PC Sabeti Genetics SR, Grossman plots. JJ, manhattan pipeline. Vitti practices and best Q-Q Toolkit C Analysis using Hartl Genome MO, results the Carneiro GWAS GA, visualizing Auwera der for Van package R using an monsoon Asian qqman: East BioRxiv and (2014) China SD over Turner climate maximum glacial last Revisiting simulations. World’s (2016) PMIP3 the D reveal Jiang wells water Z, neolithic Tian Early (2012) U polymorphism. Buntgen architecture. DNA H, wood Stauble on D, oldest size Hakelberg population R, in Elburg W, change Tegel of effect The agro-ecosystems. (1989) in F pathogens Tajima plant of origins The Phytopathology (2008) of BA fungal McDonald the EH, of Stukenbrock domestication and Origin of (2007) 398-411. population BA , a McDonald in M, pathogen Javan-Nikkhah diversity wheat S, sexual Banke of E, characterization Stukenbrock Molecular (2013) H Kauserud lacrymans Serpula S, Maurice I, Skrede fungi pathogenic forest the MC Walter in AN, Prasanna G, Sipos Himalayas. the SA in Elborne ) J, Bech-Andersen J, Singh Fg1) )aaye fasprt aasto nyJpns tan,clrdb egahcoii from origin geographic by colored strains, K Japanese by only separated of was set set data data full separate (Hokkaido). the a N when of or Europe analyses (Honsu) from c) groups S S1). 1d), two Figure (Fig the Supplementary by 4 see colored = error; strains, validation cross European lowest only the = of with K those to individual) set. (i.e. one lacrymans 7 data for = full assignment K the 2 the and from shows Figure 5, indicate derived bar = are charts (each K charts pie from isolates 4, pie smaller 36 included = small were all K Admixture. the the for 2, isolates software 2), and assignment two = separately the the only K analyzed demonstrate As using not (Admixture d) separately. groups were set analyzed they assignment data was Zealand, genetic full population New each show the when from a-c structuring results genetic indicate Zealand. charts New pie and Large Japan Europe, in 1. Figure LEGENDS FIGURE iri O:10.1101–005165. DOI: biorXiv , LSBiology PLoS , rnia opnn nlsso 1,9 Nsfo 6ioae ftedyrtfungus rot dry the of isolates 36 from SNPs 419,196 of Analyses Component Principal . 47 )aaye ftefl aae,clrdb egahcoii )aaye fasprt aaset data separate a of analyses b) origin geographic by colored dataset, full the of analyses a) . egahcdsrbto fteicue sltsof isolates included the of distribution Geographic otaplacenta Postia ora fItgaieAgriculture Integrative of Journal , 97-120. , 77 yoparlagraminicola Mycosphaerella 4499–4507. , , Mycologist erplrbasidiomycete. tetrapolar a , aaoegah,Pleciaooy Palaeoecology Palaeoclimatology, Palaeogeography, 46 75–100. , , 4 LSONE PLOS e72. , and Armillaria , 7 hnrcat chrysosporium Phanerochaete 124–130. , tal. et , 7 tal. et . e51374. , 21)Gnm xaso n ieg-pcfi eei innovations genetic lineage-specific and expansion Genome (2017) tal et aueEooy&Evolution & Ecology Nature i ypti speciation. sympatric via tal. et 19)Tesac o iddyrtfnu ( fungus rot dry wild for search The (1993) , 21)Sgicn leaino eeepeso nwood in expression gene of alteration Significant (2011) . 3 ee,Gnms Genetics Genomes, Genes, G3: 14 21)Fo at aat ihcndnevratcalls: variant confidence high to data FastQ From (2013) 1673–16 , 15 urn rtcl nBioinformatics in Protocols Current epl lacrymans Serpula ypatspecies. plant by oeua ilg n Evolution and Biology Molecular , , 453 1 1931–1941. , 115–126. , ple n Environmental and Applied rmtebitenvironment built the from , Genetics 3 145–152. , nulRvesin Reviews Annual epl lacrymans Serpula , , 43 nulReview Annual 123 11.10.1–33. , 597–601. , Serpula , 24 Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. serpula-lacrymans demographic-histories-revealed-in-two-invasive-populations-of-the-dry-rot-fungus- Table_3.pdf file Hosted serpula-lacrymans demographic-histories-revealed-in-two-invasive-populations-of-the-dry-rot-fungus- Table_2.pdf file Hosted serpula-lacrymans Japan from demographic-histories-revealed-in-two-invasive-populations-of-the-dry-rot-fungus- experiments loss mass loss percent Table_1.pdf mass the the indicates decay. in axis of file y included days The Hosted 60 isolate after respectively. one blocks (green), and wood Zealand the four New of and Five, (blue) Europe Zealand. (yellow), New and Japan Japan. from 8 isolates Figure of D Tajima’s d) and a) isolates windows. genomic kb 10 for number indicate axis 7 x Figure in Distance R decay. while linkage pairs, Japanese indicate base yellow of while the decay Beagle. of linkage scaffolds. parts European using the the indicates represents strains yellow x-axis dikaryotic while The and 6 the population, Figure ID-a European population. from the Japanese Strain SNPs to the the assigned to PCAdmix. genome phasing assigned with the genome after estimated of haplotypes parts populations different indicates Japanese two Blue and the European indicate the -b to ICMP18202) TBot diverged.and bottleneck. populations the effective current of since 5 size The time Figure population AIC. indicates lower effective TDIV the a bottleneck, indicates with 10 Bot probable since while most used, time N, the indicates were with is annotated rates bottleneck is a mutation size by population different followed split Two population a populations. with European D and a) Japanese scaffolds. adjacent 4. the Figure separate dots grey and Black genome. lacrymans 3. Figure ikg ea fteErpa n h aaeepplto of population Japanese the and European the of decay Linkage : ahta lt fncetd diversity, nucleotide of plots Manhattan . h oddcyrtsof rates decay wood The . h eoi sineto h w sltsof isolates two the of assignment genomic The . sn 0k eoi idw ln h 0lretsaod fteEuropean the of scaffolds largest 30 the along windows genomic kb 10 using h he ieetmdl sdi atica2we oeln h eorpi itr fthe of history demographic the modelling when Fastsimcoal2 in used models different three The ahta lto D of plot Manhattan vial at available at available at available 2 niae ikg disequilibrium. linkage indicates π fErpa slts b) isolates, European of https://authorea.com/users/396476/articles/509636-contrasting- https://authorea.com/users/396476/articles/509636-contrasting- https://authorea.com/users/396476/articles/509636-contrasting- XY n F and epl lacrymans Serpula ST ewe h uoenadJpns ouain of populations Japanese and European the between π, 16 n aiasDaogtegnm of genome the along D Tajima’s and π nsrc,fi n iefrioae rmEurope, from isolates for pine and fir spruce, on fioae rmJpn )Tjm’ fEuropean of D Tajima’s c) Japan, from isolates of epl lacrymans Serpula XY )F b) , epl lacrymans Serpula ST . rmNwZaad(l950 (sl Zealand New from -7 n 10 and .lacrymans S. epl lacrymans Serpula leindicates Blue . -8 h model The . Serpula S7.3 Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. d) a) K =7 K =5 K =4 K =2 European population Europe New Zealand 17 c) b) Japan Japanese population New Zealandpopulation Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. c) b) a) −0.6 −0.4 −0.2 PCA 2: 9.66%−0.4 of−0.2 variation explained PCA−0.9 2: 16.30%−0.6 variation−0.3 explained PCA 2: 4.67% variation explained 0.0 0.2 0.4 0.0 0.2 0.0 −0.4 −0.2 PCA 1:49.82%ofvariationexplained PCA 1:9.99%ofvariation explained PCA 1:33.43%ofvariationexplained −0.2 −0.1 0.0 0.0 0.0 18 0.2 0.2 0.1 0.4 0.4 0.6 Japan N Japan S Ne J Europe Europe GR2 Europe GR1 apan w Zealand Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary.

ICMP18202-b ICMP18202-a 950-b 950-a TDIV 8474 gen N Fst Europe vs Japan Dxy Europe vs Japan = J A 1 a 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 1 p I 8 a C n 3 = 1 7 4 1 B N 8 E 5 o = u 9 t 1 r

0 2 o 3 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0

0 p 2 e 4 1 1

TBot 657 12345678910

TDIV 8374 N 2 2 J = a A 1 p 0 I a C 4 n 2 = 4 7 2 3 3 B 1 o 5 N t 0 E

5 9 = u 8 r 1 o 0 p 3 4 4 e 3

TBot 197 5 5 TDIV 3067 N 19 J = Chromosome Chromosome a 1 6 6 p 2 A a 5 n I 0 C 0 = 7 7 7 1 TBot 3519 N 5 E 6 = u 0 1 r 9 o 2 9 p 7 8 8 e B 3 o t

TBot 324 6 9 9 10 10 11 11 1 121314151617181920andhigher TDIV 18770 N 12 12 = J a 1 p 0 13 13 a 6 n 5 9 6

TBot 18701 15 15 N E u = 17 17 r 9 o 9 p 0 e 19 19 4

TBot 3124 23 23 B o t

3

Growth 7 Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary.

R2 Tajimas D Japan Tajimas D Europe pi Japan pi Europe 0.2 0.4 0.6 0.8 0.000 0.005 0.010 0.015 0.020 0.000 0.005 0.010 0.015 0.020 − − − − 0 2 4 0 2 4 4 2 4 2 0 1 1 1 1 1000 2 2 2 2 3 3 3 3 2000 4 4 4 4 distance 5 5 5 5 Chromosome Chromosome Chromosome 20 6 6 6 6 3000 7 7 7 7 8 8 8 8 9 9 9 9 4000 10 10 10 10 11 11 11 11 12 12 12 12 13 13 13 13 5000 15 15 15 15 17 17 17 17 19 19 19 19 Populations 23 23 23 23 Japan Europe Posted on Authorea 18 Feb 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161363779.98341786/v1 — This a preprint and has not been peer reviewed. Data may be preliminary.

% mass loss 20 40 60 0 18015 Spruce

SL43528113 SL4453SL198 SL1984SL393 SL3935SL420 SL4206Mbgt1

Mbgt17S7 S78SL187 9SL200

SL187ICMP18202 SL200 ICMP18202 20 40 60 0 18015 Fir

SL43528113

SL4453SL198

SL1984SL393 21 SL3935SL420 SL4206Mbgt1

Mbgt17S7 S78SL187 9SL200

SL187ICMP18202 SL200 ICMP18202 20 40 60 0 18015 Pine

SL43528113 SL4453SL198 SL1984SL393 SL3935SL420 SL4206Mbgt1

Mbgt17S7 S78SL187 9SL200

SL187ICMP18202 SL200 ICMP18202