A Narrow Window for Geographic Cline Analysis Using Genomic

Home , Cline (biology), Deme (biology)

Posted on Authorea 11 Sep 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159986500.06995807 | This a preprint and has not been peer reviewed. Data may be preliminary. itrsciesae n nrae ohflepstv n as eaierts nodhbi oe,genomic zones, hybrid old In rates. negative divergence, false genomic modeled overall and under increases We positive evolving drift false and zones, both hybrid clines. rates, increases young migration geographic and in and shapes that using sizes, found cline deme We detection of distorts age, genetic selection. negatives robustness distinct on of false with the drift types zones of different evaluate and versa. hybrid effects to positive stone vice the stepping approach measured outlier-based false and multiple We simulation selection other on scenarios. individual-based under with and evolutionary forward-time different be As differentiation, under a to analysis use appear introgression. and cline signatures we regions hybridization of geographic putative study, of identify neutral patterns studies to make this baseline for used can In from mainstay widely histories a is deviations demographic is zones detecting approaches, outliers hybrid by for natural selection scan of to analysis of data cline phenotypic Geographic and speciation. genomic of use The NC. Hill, Abstract Chapel Carolina, North of [email protected] University Biology, Email: of Department 43230, , Jofre Hidalgo I. Calnali Gaston 392, Septiembre de Correspondence 16 “Aguazarca”, Huastecas las Mexico, de Cientıficas Investigaciones arwwno o egahccieaayi sn eoi aa ffcso g,sz,admgainon migration and size, age, of 1 Jofre effects I. data: Gaston genomic Authors: using analysis individuals. cline hybrid geographic rates of suggest populations error for results large Our window with narrow zones higher. hybrid are A young distortion false in cline both analysis and increases outlier divergence and for genomic selection. shapes useful zones, of cline most multiple hybrid types distorts are modeled old different divergence, clines We In under genomic geographic evolving overall that rates. clines. and increases negative drift rates, drift to geographic false of migration zones, approach using and hybrid and effects positive simulation detection young sizes, the individual-based negatives in deme measured that forward-time age, false We found distinct a and We with scenarios. use positive zones evolutionary we false hybrid regions different study, stone on neutral stepping under this from and make analysis In deviations differentiation, can cline detecting genetic histories versa. geographic by on demographic vice of selection approaches, and robustness of outlier-based signatures the selection other putative evaluate under identify with be Geographic to As to speciation. used and appear hybridization introgression. widely of is of studies for zones patterns mainstay hybrid a baseline is natural outliers for of scan analysis to data cline phenotypic and genomic of use The Abstract 2020 11, September rates 1 error on migration Jofre Gaston and size, genomic age, using of analysis effects cline data: geographic for window narrow A eateto ilg,TxsAMUiest,TM,CleeSain X783 USA, 77843, TX Station, College TAMU, University, A&M Texas Biology, of Department ea & nvriySystem University A&M Texas 3 eateto ilg,Uiest fNrhCrln,Cae il NC Hill, Chapel Carolina, North of University Biology, of Department 1 n i Rosenthal Gil and 1,2,3 i .Rosenthal G. Gil , 1 1,2 1 2 etode Centro Posted on Authorea 11 Sep 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159986500.06995807 | This a preprint and has not been peer reviewed. Data may be preliminary. omdlhwhbi oepoete ffce ule eeto,w sdAmxe Cie l (2016) al. et (Cui admixed Admix’em of used simulations realistic we generates detection, program outlier This affected https://github.com/melop/admixem). properties zone github: hybrid ; how model To modeling and Simulation false of rate Methods scenarios. the and evolutionary regions and Materials different detection of under zones positive shapes demographic hybrid different false cline with stone of zones stepping the the hybrid rate multiple multiple modifies cline along model the in have We drift simulations fixation calculate using to histories. often clines to local regions geographic how genomic aim causing in neutral and we detection 2016), negative causes Specifically, deme selection, drift small under genetic al. selection. example, often regions under et For how of evaluate (Hossjer selection. we characteristic inbreeding study, by shapes this increase caused In not rates zone. outliers of migration remains hybrid spurious model low shapes generate given cline and thus a zone sizes can hybrid of the drift on instead Thus, selection and alone size. of Migration drift cline deme models of in one and and result used deviation rates, (2011) (2018) the migration the Barton al. be sizes, that unexplored. et and can deme Sciuchetti show Polechova different locus and and of given (2011) center. effects genotypes Barton a expected and hybrid of Polechova the However, against width in selection. selection causes in shift drift reduction modeled that a and and (2018) showed and center (1975) width Maruyama width, al. the Barton and expected et reducing and Slatkin Polechova the Sciuchetti 1), and 1975; (1975) in Figure Maruyama Felsenstein reduction and (see 2018). Slatkin a shape 1975; al. cline (Felsenstein et direction distort Sciuchetti either 2011; can in shifted drift center centers have genetic the can shifting that 1985). introgression show Hewitt of and rate models (Barton high Cline Theoretical indicate cline that the 2008). (Payseur loci of widths outlier al. reduced end Specifically, have and et either 2017). species 2018); towards null Gay parental al. al. between the across 1986; et isolation et Stankowski represents easily reproductive Barton Sciuchetti 2010; in gradient 2010; (Payseur pass and involved outliers spatial are Szymura to considered rate that a are 1985; expected loci maximum null across outlier Hewitt are the the from frequencies and alleles indicates deviate their (Barton which Neutral that in shapes selection cline, changes 1993). no the the indicates and Gale of of which and diffusion), expectation width cline, (Barton (neutral the the and cline frequencies of and (Szymura center the allele allele, selection the in each under parameters, change on two potentially of uses acting 2019). loci analysis selection Geographic detect the al. of to 1985). simplest, et direction shapes Hewitt its Lipshutz At and and may 2017; Barton which positions 1986). 1), Barton 1977; cline al. (Figure Endler compares gradient et 1948; analysis spatial Stankowski more draw (Haldane a cline genome 2017; parameters across and the environmental frequencies of al. zones ancestry-allele with regions More covary in et outlier hybrid changes detect (Ryan 1993). addresses wild to Parsons introgression theory end across 1989, to same Cline the Szymura resistant introgression to & or employed phenotypic Barton widely permeable detect been selection, has sexual to theory asymmetric cline used recently, (e.g outlier been selection using about long identified inferences be has can theory that signatures Cline leave can Martin selection 2016; of Presgraves types and methods. different (Muirhead alleles identification zone Alternatively, These against hybrid selection 2017). 2020). a event, Jiggins across Matute hybridization of differentially and and a introgress offspring After Coughlan can viable 2005; selection 2013). by (Mallet generate favored al. boundaries and et species Abbott reproduce maintains 1985; individuals introgression Hewitt and distinct (Barton genetically ancestry two mixed when occurs Hybridization for useful zone most tension are genomics, individuals. Introduction ecological clines hybrid drift, geographic of migration, that populations analysis, suggest large outlier with results Keywords: zones Our hybrid young higher. in are analysis distortion outlier cline and divergence 2 Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. egahccieanalysis cline interaction. Geographic BDM in and selection, the underdominant of under range package R interquartile the and per-locus using range, calculated and (1984) we F Cockerham differentiation, and index Weir genomic fixation in Wright’s degree calculated (1000 the we increasing zones selection, hybrid demes, old of among and differentiation models generations) (100 between young and between differentiation generations), genomic in variation compare To using in differentiation codominance genomic assumed of C). We Patterns S1, is modeled (7.5). Figure the fitness We relative Information seven in where . one Supporting chromosome fitness, 2004) loci, in on additive Orr autosomal coefficients applied another two and and and between (Coyne alleles interaction (3.5) incompatible fitness BDM the three hybrid a chromosomes reduced simulating of of by interactions cause middle epistatic common of more effects a 1937; the be (Dobzhansky may incompatibilities 1940) (BDM) Muller Bateson–Dobzhansky–Muller selection, underdominant Unlike incompatibility Bateson–Dobzhansky–Muller C) loci. focal specific the at genotype Sdhfre l 06,te ota ipeseai nwihhbisaeufi.W sue additive assumed We unfit. are hybrids nature which in in unrealistic are scenario models simple selection a is underdominant portray fitness Although relative they chromosomes where of 2016), 9.5. middle fitness, and the al. 5.5 in et as loci heterozygous (Sedghifar on direc- denoted as underdominance chromosome modeled B), nine, on We modeled S1, and We another Figure gradient. and five Information gradient. spatial 3.5, spatial (Supporting as the underdominance the denoted along modeled along three, We allele disadvantage chromosomes of other 7.5. middle as the Figure the denoted than Information at incom- seven, fitness locus (with (Supporting lower one selection on selection having directional selection allele directional of tional one effects modeled as the We A) modeled we S1, underdominance. hybrids, and on dominance) selection ancestry.plete of to effects respect the with determine selection To no selection of underdominance expectation null and the Directional with B) above described as simulations the ran We 2). selection: Figure No (see A) selection zones: to of hybrid sizes type performed in deme We each selection the 0.01. for restricted of and combination, We 0.1 Models parameter to rate. restricted each migration and with and symmetrical was simulations size rate replicated deme Migration 100 the after individuals. modifying 1,000 removed by and were 500, drift individuals 100, of parental effect hybrid generation the old each varied (for We of generation end thousandth the and and at generations zones), overlap; 1,000 hybrid mating. not for young did mating (for random Generations randomly allowed markers hundredth We 11 zones). the in total. in ancestry in tracked We individuals markers recombination sampled 110 (2008). This Payseur chromosome, and each meiosis. Dumont in by per suggested distributed arm that per to event similar recombination is rate randomly-drawn one with each chromosomes, rteohrall ilb ls ofiain(e lti n auaa17) n hl epn nadequate proportion an ancestry keeping an while has and deme 1975), admixed one Maruyama each one where 1 and centers, from at generation Slatkin increasing cline at (see each 2 their that demes fixation population assumed from hybrid populations, We to away of source close boundaries . number be with speed large the will computation clines restricted infinitely allele model We two other to 1). the 1975), and Table Felsenstein or simulations, Information demes to all Supporting (similar 19 For 2; 19 with (Figure 2018). to cline cline al. the a et of Schumer in extreme 2017; admixture Massey modeled 2016; Brandvain we and (Schumer populations diploid p 00 to =0.05 f 1 = F ST − F p ST x F ausfo 0 oiwt oslcin ne ietoa selection, directional under selection, no with loci 100 from values 09 ln h ln seFgr 2) Figure (see cline the along =0.95 3 ST . , 5 hl irto ostervre(feo 04.T estimate To 2004). (Efremov reverse the does migration while − x 5 . 5 − 3 pegas x 7 . 5 Prds21) ecluae h en median, mean, the calculated We 2010). (Paradis − x 9 F . 5 ST where , mn l yrdppltosfollowing populations hybrid all among x f safnto fa individual’s an of function a is . 1 = h eoe osse ften of consisted genomes The − x 3 . 5 ST − x rf generates Drift . 7 . 5 seselection (see p from Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. irto ae erae eei ieetain oegnrtosi ditr,b otat increased contrast, by admixture, in generations mean on More effect differentiation. an differentiation. S2) genetic also genetic Figure parameter had decreased Information model admixture rates each Supporting in migration of generation 3; Table effects and the Information rate, migration compared Supporting we 3; differentiation, (Figure genetic differentiation on drift of on effects the observe differentiation To genetic hoc in post parameters performed model hybrid of then the We Effect from negatives. data false the and omitted positives we on Results true model, parameters linear no of these FNR are means the of there estimated For effects of since R. comparisons the selection, in function no analyzed lm with then the We zones with admixture. FNR of and generations FPR, and rates, migration in parameters five following the estimated the we in cline, a algorithm fit Metropolis–Hastings To The † genotyped. to markers analysis. (https://github.com/gjofre/simulation_clines) 110 cline scripts the defined geographic from the custom for individuals from used package random necessary ancestries then R with 30 files We file sampled input output we the files. an outliers, generates generate input shape Admix’em the cline 1,000. in on and markers drift 100 generations and in migration deme of each effects the study To efitdalna oe oosrewihhbi oeprmtr ( parameters zone on hybrid effect higher which a observe had to selection) were of model that type linear selection as a of flagged fitted form We were each that under loci loci of neutral analyses proportion of Statistical the proportion 2). as the table (FNR) as SI rate (see (FPR) negative replicate, undetected each rate false For false the S2). the positive Table and as than false Information Supporting outliers average lower selection (see was the without zone cline. hybrid calculated width markers each genome-wide we for their the categorized matrix to if we error compared an Finally, and computed discordant We cline. cline, or index non-coincident index center were hybrid hybrid their they genome genome if catego- if We positives whole whole positives otherwise. true the the negatives as of of false incompatibilities center width as BDM and the in shifted fitness and with center higher cline selection coincided with the underdominant displayed gradient under they geographic markers if the rized positives of true side as under the 2). selection regions towards Table directional and Information under positives, markers (Supporting false categorized negatives or We false negatives true or as positives regions true neutral as categorize selection to us allowed This intervals. center only estimated I ( Model tails combinations. cline parameter the cline of size the and oetACgnm-ieaeaeciemdli zr etr n itso n w lnswr considered were clines two any of confidence widths 95% and the Centers if hzar. outlier in either an model (same of considered cline coincident was value average marker genome-wide AIC A AIC lowest genome. lowest the the across for outliers intervals for scanned Akaike replicate. then each We corrected for lowest estimates cline average the average the analysis with genome-wide used detection a then model Outlier We estimate The marker. to each steps. parameters for 100,000 the chosen of all was of burn-in (1998)) Akaike a (AIC, after criterion information steps MCMC 500,000 using estimates and θ ln width cline , 1and = F P ST min ausars elctdhbi oe.Udroiac n D noptblte rae genetic created incompatibilities BDM and Underdominance zones. hybrid replicated across values and θ B hzar and ) n nlddfie ns( ends fixed included and 0), = P w max h nso h cline the of ends the , Dryer ta.21) a sdt tgorpi lnst leefeunisfrec of each for frequencies allele to clines geographic fit to used was 2014), al. et (Derryberry B † loe ovr.Ec oe aaee a siae sn he needn hi runs chain independent three using estimated was parameter model Each vary. to allowed rcnodn (same concordant or ) rmtedt,adasmdn al.MdlIIwstesm sMdlI,adwt tail with and II, Model as same the was III Model tails. no assumed and data, the from B P 1 and F ST P B F P,adFRi ahhbi oemdlparameter. model zone hybrid each in FNR and FPR, , min P w ST 2 fterprmtr vrapdwt ahohrs9%confidence 95% other’s each with overlapped parameters their if ) o opttoa pe,w te he oeswt different with models three fitted we speed, computational For . P,adFR efis o ovre h ieetdm sizes, deme different the converted log first We FNR. and FPR, , and P min w P or and max † 4 i o vra ihtecndneitraso the of intervals confidence the with overlap not did P h aea hc h ln aldecays tail cline the which at rate the , max xdt eoadoe.MdlI estimated II Model one). and zero to fixed † n width and N , F m w ST. rmtedt,asmdn tails no assumed data, the from eeaino ditr,and admixture, on generation , agrdm ie n higher and sizes deme Larger hzar ln center cline : θ . P eesize, Deme 1 and F † θ ST , P w 2 , , , Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. eue irto ewe daetdms oemresfie ln h egahcgain,rsligin resulting gradient, geographic the along fixed markers some higher ( demes, low had rates adjacent zones between migration hybrid migration low Old reduced with D-F). zones S2 hybrid Figure wider Old Information and (Supporting higher sizes had narrower sizes deme and deme bigger small with patterns with zones generate zones hybrid and hybrid selection, sizes directional population Under small regions. genomic with neutral zones in hybrid decreased selections in of rate differentiation migration genetic inflate higher drastically a A-C). having S2 and Figure sizes, Average selection. deme for small need any with without differentiation genetic high found We ihsalpplto ie shg nbt on n l yrdzns eadeso irto ae.I old In rates. migration of regardless zones, hybrid zones old hybrid and in false young misidentification the than both of size) than in larger risk deme larger high The zones large is 4e). sizes hybrid and sizes (Figure. migration population risk population replicates high lower small with across with have with 1.35% especially zone averaged will hybrid still zones, zones (young rate hybrid conditions hybrid positive favorable old young 0.1. most than than hybridization, hybrid the less positives natural young Under of in false analyzing FPR was when generating mean scenario that of with best rates, suggest The migration 0.58. results high of These values and FPR sizes average deme had ( large still sizes with rates zones deme migration small low with with zones zones inflated hybrid highly old which Specifically, ( 1), ( rates showing Video A). migration Information shifted, S3, low drastically Supporting Figure and centers ; 100) Information B their & with (Supporting A clines FPR 4, most the (Figure the introgression generated of sizes patterns 3). deme spurious Table small Information with Supporting Supporting zones 3; 3; Hybrid Table (Figure Information values hybrid FPR Supporting in 3; mean 0.98) (Figure on FPR rates effect (mean migration FPR S2) highest low the Figure and with sizes Information distribution, deme FPR small the on with effect zones strongest the detection had size positive Deme false on parameters model of showed Effect incompatibilities, differentiation. BDM genomic or of underdominance patterns via either consistent genotypes, more hybrid against 1000 Selection sizes. at deme selection, ( directional mean under rates affect reducing zones not migration hybrid did low the sizes the and to deme admixture Similar small of BDMIs, G-M). with generations S2 or Figure selection, Information underdominant (Supporting differentiation. under low zones of hybrid patterns In show yet and selection directional under eectgrzda reotir FR=0 uprigIfrainFgr 4.Ee hnditmodifies drift when Even S4). Figure Information Supporting sizes 0; population = with (FNR zones hybrid outliers (Supporting all true gradient In as the 2). of categorized Video side were Information opposite Supporting the Drift B, than to zones. and shifted larger hybrid A rarely young admixture. S4 were in centers 3) of Figure elevated Table but was Information generations Information which shape, fewer FNR cline (Supporting overall did distorted FNR low indeed as overall showed simulations the selection FNR, our directional increasing average under across slightly lower Markers effect, FNR showed minor of sizes a risk deme had highest bigger rate the Migration with had zones incompatibilities Hybrid BDM . and underdominance detection with negative Loci false on parameters model of Effect positives. false identifying of N 00 a rsi eraei P,btol hnte a irto ae of rates migration had they when only but FPR, in decrease drastic a had 1000) = F ST aus hs eut ugs hti l yrdznswt eue irto ae akr a be can markers rate, migration reduced with zones hybrid old in that suggest results These values. F ST N= F aus oee,ti ffc apndol tafwlc n nyi yrdznswt small with zones hybrid in only and loci few a at only happened effect this However, values. ST 0,adi l yrdznsatr10 eeain,almresudrdrcinlselection directional under markers all generations, 1000 after zones hybrid all in and 500, F itiuin hnyughbi oe,btol hnmgainrtswr ih( high were rates migration when only but zones, hybrid young than distributions ST auspae nodhbi oe ihlwmgainrts( rates migration low with zones hybrid old in peaked values . oegnrtosi ditr loicesdFR h oeo eeto a no had selection of mode The FPR. increased also admixture in generations More N= m= F 0,hvn irto ae agrthan larger rates migration having 500, m ST .) eosre gi neeto rf nodhbi oe drastically zones hybrid old in drift of effect an again observed We 0.1). 00)hda vrg P f09.Odhbi oe ihlredm sizes deme large with zones hybrid Old 0.98. of FPR average an had =0.01) itiuinbcm arwri ohhbi oe ihhg ( high with zones hybrid both in narrower became distribution m 00) a rsial erae average decreased drastically had =0.01), 5 F m= ST ute Spotn Information (Supporting further . ilide eraeterisk the decrease indeed will 0.1 F ST a ihs nhbi zones hybrid in highest was F m= m ST ..Odhybrid Old 0.1. = F itiuinthan distribution ST .1.Ditcan Drift 0.01). aus With values. m N= m =0.1). =0.1) 500. F N= . ST Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. ml eeszscnas itr u seseto o eeto satn,ee ncssi hc ecan we which in have cases migration in restricted even and acting, sizes is deme small selection even with how where zones of rate, Hybrid assessment migration selection. our under low positives. distort regions with rates. false identify drift, also zones correctly positive can of of hybrid false the sizes effects rate old high deme from maintain the in the away Small can sufficient decrease centers significantly drift not sizes, the does reducing is population shifts size and FPR large al. suggesting and population with clines, in et deme, rates, the reduction coincident Sciuchetti a positive Increasing this and and within However, false 4). (2011) concordant fixation Barton (Figure high of more and cline show risk generating Polechova index increases rates by hybrid drift results migration that the expected low found to and we Similar sizes analyses. (2018) genomic cline deme decrease Migration for substantially small ages. limitations sizes with negatives. zone deme genome and zones hybrid large the positives the having Hybrid false scanning ultimately, as least when but, further the positives role even produce important increases and false differentiation differentiation an of This also rate plays i the under rates selection. regions increases of genomic turn to signatures similar in for regions in genomic differentiation variance neutral Genomic in high differentiation selection. causes of patterns drift creating the hybrids, represent upon that loci show outlier that comparisons likely less Our even spurious selection. it generate of making can evidence selection, zone, as of drift taken hybrid effects candidates. selection, be the a robust could of obscure that of to absence introgression analysis act age) the increased can and or cline In drift Conversely, reduced rates rates. migration geographic of migration low negative patterns makes with strong sizes, false zones with (deme drift and hybrid outliers demography positive older that drift the for false as that suggest on increases well showing depending drift results as that, studies sizes, Our and deme show 2018) We small Nagylaki zones. al. with rates. hybrid 1975; zones et hybrid Maruyama in Sciuchetti any for and 2011; clines inappropriate Barton Slatkin spatial and 1975; distort (Polechova (Felsenstein 2011). can empirical Barton theoretical and and used with (Polechova 1980) have zones consistent Lucier hybrid studies are from (Payseur Numerous shapes results patterns dynamics. cline ancestry Our distort average selection can from of demes outliers within detect range frequencies drift to a allele However, analysis how 2010). given cline about geographic gradient with predictions spatial data powerful whole-genome a makes 1985) across Hewitt change and should (Barton theory cline Geographic incompatibilities selection. BDM underdominant under in deme involved markers large interval markers having to Discussion confidence rates, that compared index migration negatives, suggest hybrid low false results the with fewer These zones outside generate FNR. hybrid were will the old clines In drastically the &C). decreased but the A ( sizes degree, when had S6 lesser FNR Figure sizes highest a Information the deme to showed (Supporting rates, shifted large migration centers high with cline with zones zones The hybrid hybrid old Young hand, other 4). underdominant the to Video relative lower Information slightly Supporting lowe was FNR 3; average (Figure the zones, selection incompatibilities directional selection hybrid BDM under in young markers involved to and markers similar In small patterns 3). with in clines Video that generate Information suggest can Supporting drift results (e.g. zones, These hybrid with old zones S5). hybrid in in Figure and example, Information For reduced. (Supporting substantially centers not was (e.g. of FNR sizes sizes sizes deme ( deme (Sup- deme small larger sizes zones with with deme zones hybrid even small hybrid and all Old zones, FNR, rates. hybrid across migration young FNR of In hybrid regardless increased young C). FNR, showed in S3 selection Figure only Information and underdominant low porting under is markers FNR contrast, on By impact the sizes. selection, deme directional small under with markers zones of shapes cline the st FNR sp , N= cfial ihhg irto ae Spotn nomto iueS ,sldsurs.On squares). solid D, S3 Figure Information (Supporting rates migration high with ecifically 00 eadeso irto ae,˜0 ftemreshddatcsit ntercline their in shifts drastic had markers the of ˜40% rates, migration of regardless 1000, 6 F ST eadeso h yeo eeto acting selection of type the of regardless N N 0)datclyincreased drastically 100) = 10 hwdtehighest the showed =100) N 10ad500). and =100 Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. .Ms,S uln .Ncos .W ot,C aio,K fni,A .Rc,M .Rthe .Seifert, B. Ritchie, G. M. Rice, M. A. Martinez-Rodriguez, Pfennig, P. K. Mallet, Parisod, J. C. Marczewski, Nolte, T. W. Hermansen, Keller, S. A. B. C. J. Nichols, Brelsford, Jones, Cahan, R. A. H. J. Mullen, Boughman, S. Jiggins, W. Grill, S. C. J. A. Most, Bierne, Eroukhmanoff, Hudson, M. F. N. G. Dieckmann, Baird, A. U. E. Butlin, Hewitt, J. K. S. G. R. Arntzen, Buggs, W. R. J. Buerkle, Ansell, A. S. Albach, D. R., Abbott, A&M Texas at lab Blackmon the References and center particularly Computing R01GM121750, analysis lab, Research award Computation Performance Matute fellowship. NIH James student High University. the by to international the and CONACyT supported grateful at a was lab are conducted and We R. Rosenthal were 1755327, analysis. G.I.J. and the computation comments. 1354172 of awards the insightful members NSF provided for and server who his Winemiller, Matute, thank- use deeply Kirk Daniel are us Delmore, We letting Admix’em. Kira for for Cai, needed Blackmon files Heath configuration to example sharing ful for Schumer Molly studying thank We for framework powerful a of analysis Acknowledgements importance cline the geographic independent overestimate introgression. make with to of combined can us patterns demographics, outliers, lead genome-wide zone of may hybrid validation zones of hybri- or hybrid consideration historical of replication of Careful and analysis evidence therein. Hybridization spatial pervasive processes genotypes. show but introgressi- adaptive recombinant taxa adaptive genome, many like against the and look selection in selection, that or dization by Our negatives alleles favored selection. and frequently of of positives are movement evidence introgression false neutral facie both prima than generate as rather taken can and on, often phenotypic drift loci. sizes, is that to of increased genes tract suggest number comes candidate to ancestry results small it or a susceptible traits when increasing of with ancestry, patterns are introgression associated similar excess Asymmetric methods are see generating differences these to et by interspecific of expect (Sedghifar when cases should All particularly lengths these we introgression, 2018)). Further, tract in densities. al. ancestry drift, junction ecological et to 2011), reducing and (Hvala evolutionary due Buerkle junctions in rates and used ancestry temporal error methods (Gompert and or detection clines outlier 2016), 2015) genomic of al. 2018). al. family example al. et a et for of Janousek Ryan one genomics, multiple 2015; 2014; is across al. al. analysis et outliers cline et (Taylor same Geographic candidates Dufresnes the outlier 2014; organism of on al. validation selection model et with of the (Schumer analyses helpful zones of most hybrid is history with independent analysis zones demographic cline hybrid the Geographic formed recently Knowing populations. in individuals. appropriate hybrid hybridizing most priori or is of analysis drift populations cline reflect geographic large that instead suggest may results Miller introgression and Our (Hamilton adaptive change evidence apparent climate as to directional invoked that resilience been or indicate of incompatibilities. has and introgression, simulations introgression 1993) analyses adaptive adaptive al. Our spatial Putative et of 2016). (Parsons species. loci, importance selection parent BDMI sexual the one asymmetric and from overestimating of underdominant allele markedly on an be negatives on may selection false gradient. zones and the hybrid neutral of of on side gradient, fit) positives under geographical less false regions the (the Between genomic of opposite sizes, side misinterpreted adaptive the deme be the towards small towards also shifted with shifted could centers centers replicates showed which having our 4), of Supporting of instead and (e.g. ˜3% gradient adaptive selection, 3 the in directional Videos of (e.g. Additionally, side Information selection. either selection and Supporting to directional center underdominance of S6; as the and with shift type lower and S5 have zones fixation, different genotypes Figure of Hybrid heterozygous Information rate a Since the hybrids). centers. increase as against can shifted drift outliers drastically selection fitness, with masking or clines show ecotone drift, incompatibilities, an BDM by of caused instead distortion introgression of risk higher a eueters fmsdniyn eta ein scniaergosudrslcini natural in selection under regions candidate as regions neutral misidentifying of risk the reduce can 7 a Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. isuz .E,J .Mir .E erbry .J ilr .Seasn n .P erbry 2019. Derryberry. P. E. species. reversed and sex-role Seehausen, between O. zone Miller, hybrid J. a M. in Derryberry, trait E. competitive 32:1208-1220. female 73:188-201. G. Evol Evolution a Meier, Biol of Mol of I. introgression Mouse. Organization J. Functional House Differential 2015. the E., Tucker. in K. S. P. Boundary Lipshutz, and Species Teeter, the genomic C. in Shape K. May Wang, speciation Genome Y. and in the L. hybridization equilibrium Munclinger, of P. Signatures migration-drift V., 2018. Janousek, to Payseur. A. time 72:1540-1552. B. Evolution and ancestry. and Frayer, of sizes E. patterns Effective M. A., 2016. J. 112:139-156. genetic Hvala, Ryman. Biol and Popul N. management Theor and for populations. resource subdivided Laikre, geographically a L. as O., introgression 30:33-41. Adaptive Biology Hossjer, Conservation 2016. climate. Miller. 48:277-284. changing M. Genet a J. J in conservation Cline. and a A. of J. Theory Hamilton, 20:2111-2127. The ecology 1948. Molecular S. clines. genomic B. of J. estimation Haldane, Bayesian 62:2789-2806. 2011. Phenotypic Evolution Buerkle. and A. Models. Molecular C. Zone on and Tension Clines Z. on Comparing Gompert, 2008. Window Natural-Selection. Lenormand. A T. Zones: and and Hybrid Bell, Migration in A. by Traits D. Crochet, Maintained A. P. Are L., Gay, Which Clines in 10:1-246. Drift biology 81:191-207. population Genetic Genetics in 1975. Monographs one-dimensional clines. J. and and Felsenstein, island speciation, mammals. variation, in Geographic F(ST) in 1977. of A. recombination value J. equilibrium of Endler, 40:1268-1273. the rate Genetika to migration. approach genomic of of the rate models The stepping-stone of 2004. Evolution V. V. 2008. Efremov, Payseur. A. B. 62:276-294. and Evolution group). L. arborea B. (Hyla radiation Dumont, frog tree European Timeframe 15. the 2015. Biol in Perrin. zones Evol N. contact and Bmc secondary Nicolas, from L. analysis P. inferred Press. Tzankov, zone speciation University N. of Crnobrnja-Isailovic, Columbia hybrid J. Species. Brelsford, hzar: A. of 2014. C., Origin Dufresnes, Brumfield. the T. and forward-time Genetics R. for 14:652-663. 1937. and Resources framework T. Maley, Ecology Dobzhansky, flexible Molecular M. package. a J. software Derryberry, R Admix’em: an E. 32:1103-1105. 2016. using Bioinformatics G. Rosenthal. choice. P., mate G. E. and Derryberry, G. selection with and Associates. populations Schumer, Sinaeur hybrid MA: of M. simulations Sunderland, F., Speciation. 2004. R. Orr. Cui, sciences A. the Biological H. B, throughout and Series A. postzygoticbarriers J. London. intrinsic Coyne, of of Society importance 16:113-148. Royal The Syst the Ecol 2020. of Rev 20190533. Matute. transactions Annu R. Philosophical Zones. process. D. Hybrid speciation of and 13–45 Analysis M. Pp. 1985. J. zones. Hewitt. Coughlan, hybrid M. UK. G. of Oxford, and analysis Press, H. University Genetic N. Oxford 1993. Barton, Process. Gale. NY. Evolutionary York, the S. New and York, K. Zones New and Hybrid Springer 215-222 H. Akaike. Pp. Hirotugu N. Identification. of Hybridization Barton, Model Papers 2013. Statistical Selected Zinner. the eds. D. at Kitagawa, and Look G. Wolf, New and W. A B. 1998. J. H. Vainola, Akaike, 26:229-246. R. Biol Szymura, Evolution M. J J. speciation. Stelkens, and R. Smadja, M. C. 8 in in .Pre,K Tanabe, K. Parzen, E. .G arsn ed. Harrison, G. R. Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. zmr,J .adN .Bro.18.GntcAayi faHbi oebtenteFr-ele Toads, Fire-Bellied the between 40:1141-1159. Zone Evolution Hybrid Poland. a studying Southern of in for Genetic-Analysis Cracow 1986. tool near Barton. Bombina-Variegata, a H. and as N. Bombina-Bombina and analysis M. cline ecology J. Molecular Geographic Szymura, monkeyflower. a 2017. in Streisfeld. divergence A. pollinator-mediated of M. 26:107-122. study 81:209-222. and case Genetics a Sobel, cline. variation: hybrid M. genome-wide a in in J. drift blocks S., Genetic Stankowski, haplotype 1975. and Maruyama. T. lineages and clines: M. Beyond Slatkin, 2016. Ralph. 25:2559-2576. P. ecology and Molecular study. Brandvain, zones. simulation Y. A A., zones: Sedghifar, incompatibi- contact Dobzhansky-Muller secondary 2018. at Perrin. introgression N. 72:1350-1361. sex-chromosome and Evolution Sankararaman, and Brelsford, S. drive, A. Blazier, Cavoto, dominance C. E. lities, to Dufresnes, recombination J. C. with 360:656-659. Holland, interacts L., Science C. Sciuchetti, selection genomes. Skov, Natural hybrid L. 2018. of Durvasula, Przeworski. evolution M. A. the and Powell, shape Rosenthal, L. G. D. G. 3. Xu, Andolfatto, P. Elife L. Species. C. Mapping Fish High-resolution M., Hybridizing 2014. Schumer, in Andolfatto. P. Incompatibilities and Genetic Rosenthal, Molecular G. of Dresner, Hundreds populations. R. Powell, Reveals admixed D. a Cui, in R. with selection M., Schumer, epistatic associated Determining zone 2016. hybrid Patterns Brandvain. 25:2577-2591. butterfly 2017. Y. ecology Hellmann. a J. and of J. M. and landscape Schumer, O’Neil, genomic T. 26:4725-4742. S. and ecology Pfrender, 115:E2284- Molecular Hellmann. geographic E. gradient. America J. M. the climatic Scriber, of J. across M. and States J. divergence Fontaine, Emrich, United of C. J. the M. S. F., of S. Jones, Sciences Ryan, E. of simulation S. Academy and Pfrender, National collection, E. museum the M. E2291. genomics, of Scriber, Expected with Proceedings revealed M. the movement modeling. J. Narrows zone Deines, but hybrid M. Climate-mediated Cline 2018. J. Expected F., the S. Widens Ryan, Drift Genetic 189:227-U905. 2011. Genetics in Barton. involved Width. Cline regions N. genomic and Plumage identify J. Sexual to Polechova, zones Secondary hybrid 10:806-820. of in Resources Spread introgression Ecology differential Unidirectional Molecular Using speciation. 1993. 2010. Braun. A. 260:1643-1646. J. B. Science Payseur, M. Zone. and Hybrid Avian Olson, an L. Bioin- across approach. S. Traits integrated-modular J., an T. with 94:497-517. Parsons, genetics Genetics population cline. for a package in R 26:419-420. drift an formatics random pegas: of systematics:185-268. 2010. analysis new E. Numerical The Paradis, 1980. systematics. Lucier. on B. work and Drosophila T. the Nagylaki, of Genomic Bearing the 1940. and 187:249-261. J. Adaptation, Nat H. Local Am Muller, Incompatibilities, Species. Hybrid between 2016. Introgression Presgraves. Natural C. of D. Distribution Amer- and Suggests A. Genomes C. Rican Muirhead, Puerto in 81:59-77. Discordance Mitonuclear Benefit. Genet Amerindian Mitochondrial Opin Strong indian Curr 2017. introgression. E. of S. landscape Massey, genomic the 20:229-237. Interpreting 2017. Evol Jiggins. Ecol 47:69-74. D. Trends Dev C. genome. and the H. of S. invasion Martin, an as Hybridization 2005. J. Mallet, 9 Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. orsodn etr.Gntcdithsdsotdtelgtga ln,rdcdiswdhadsitdthe shifted and width its reduced their cline, denote gray locus file lines light neutral Hosted dotted the (gray), The distorted locus (yellow). has selection neutral drift directional (black), center. under Genetic genome locus whole and centers. gray), from corresponding (light clines drift geographic by distorted Hypothetical 1. Figure htt- at Dryad in available openly are study this of findings the Tables and Figures support that ps://doi.org/10.5061/dryad.0p2ngf1z9. data The writing administration, accessibility project Data conceptualization, admi- Rosenthal project G.G. draft, editing. editing. writing-original and and review analysis, review, modification, writing data nistration, simulations, conceptualization, Population-Structure. Jofre of G.I. Climate- Analysis 2014. the Lovette. for I. Contributions F-Statistics Author Estimating and 1984. Curry, Cockerham. L. C. R. 38:1358-1370. C. Ferretti, Evolution 24:671-676. and V. Biol S. Hochachka, Curr B. Zone. M. Weir, Hybrid W. Avian White, an of A. Movement T. Mediated A., S. Taylor, 10 Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. eeaemr as oiie n as eaie.NS oslcin i.–Drcinlslcin Und. selection, Directional – of Dir. distribution selection, detailed No more a - for Figure N.S. S3 Information and Supporting negatives. S2 See false incompatibility. Bateson–Dobzhansky–Muller and BDMI- positives -Underdominance, false more generate n eeaigmr as positives negatives false false and more positives generating false and only less significantly influenced produce sizes rate deme Migration large and differentiation of rates higher FNR increased incompatibilities BDM ( FNR size deme of selection, distribution of Model 3. Figure error-rates for-geographic-cline-analysis-using-genomic-data-effects-of-age-size-and-migration-on- image3.emf file Hosted times. 100 rate 100 the and migration individuals on process 30 500,1000), markers this sampled We 110 (100, same incompatibility). N BDM the size Underdominance, genotyped an and deme has Directional of deme Selection, admixed combination (No each type a 1 with generation At each zones, H19). , . infinite . non-admixed . of Two H2, rate H1, used. parameters (i.e. the proportion demes and ancestry admixed zones, 19 hybrid flank all for populations model size stepping-stone The 2. Figure error-rates for-geographic-cline-analysis-using-genomic-data-effects-of-age-size-and-migration-on- image2.emf , ihsrn eoi ieetainee ihu n edfrslcin nedmnn eeto and selection Underdominant selection. for need any without even differentiation genomic strong with m oajcn die ee,btntbc nosuc ouain.W oee 2dffrn hybrids different 12 modeled We populations. source into back not but demes, admixed adjacent to vial at available at available F ST aus FPR values, p fidvdasfo ouain2 population from individuals of https://authorea.com/users/357843/articles/480225-a-narrow-window- https://authorea.com/users/357843/articles/480225-a-narrow-window- F , ST n N ndffrn ere.Md fslcinmdfisonly modifies selection of Mode degrees. different in FNR and . l yrdznsincreased zones hybrid Old n FPR and . eesz influenced size Deme N) th irto ae( rate migration , F eeain n gi nte1000 the in again and generation, , ST ihlwmgainrtsicesn eoi differentiation genomic increasing rates migration low with P n FNR. and FPR , 11 . niiul ymtial irt ihamigration a with migrate symmetrically Individuals F ST m), F ST FPR , n eeain namxuemdf the modify admixture in generations and aus FPR values, , n FNR and th , m n FNR and . eeain ereplicated We generation. 01 .1,adselection and 0.01), (0.1, ml eeszsshowed sizes deme Small , n specifically and F ST and . Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. r on yrdznsatr10gnrtoso ditr.Oe qae r l yrdznsatr1000 after zones hybrid old are squares replicates. Open independent admixture. from of locus generations a from 100 admixture obtained from of after (black), generations is zones clines cline hybrid index with young Each hybrid zones are average hybrid histories. and are (grey) demographic squares selection different Blue no in under replicates loci 100 from Clines 4. Figure

Frequency

0.0 0.2 0.4 0.6 0.8 1.0 . 0 Generations in admixture m N m= 20 ..Oag qae r yrdznswith zones hybrid are squares Orange 0.1. 100 0.1 1000 100 40 100 0.01 Parameters 1000 Distance 12 100 0.1 1000 500 60 100 0.01 1000 100 0.1 1000 1000 80 100 0.01 1000 100 m= .1 oi squares Solid 0.01. Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986500.06995807 — This a preprint and has not been peer reviewed. Data may be preliminary. Generations selection Model m of N

FST FST FST FST 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 N.S. 100 **** 0.01 100 **** Dir. F **** **** 500 * ST Und. ns 1000 **** 0.1 1000 BDMI

FPR FPR FPR FPR 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 N.S. 13 100 False Positive Positive False Rate 0.01 ns ns ns ns ns ns ns 100 **** Dir. NS. **** **** 500 Und. **** 1000 0.1 ns 1000 BDMI

FNR FNR FNR FNR 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 N.S. 100 False False 0.01 100 **** Dir. Negative Negative **** **** 500 ns Und. **** 1000 **** 0.1 Rate 1000 BDMI