Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. fpplto itr icl.Freape ohpplto xasosadaatto edt nexcess an to lead adaptation inference and making expansions other population each both confound can example, For signals the to these difficult. 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Survey 2003; 08 n vnsurltdto unrelated events and 2008) tal. et 03 Excoffier 2003; tal. et 08 Searle 2008; tal. et et et Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. fteMdenacieaoi rsot(yradJeie20) eesl ape rmta location, that from sampled easily We collect to 2005). unable Jaenike also and were and flies) we (Dyer (though 84 invasion collect Prescott (PR, recent to possible Prescott in failed a mostly flies), archipelago suggesting surveys 48 previous Madrean Interestingly, (HU, the 1). 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Jaenike and Dyer (Dyer maximum 2005; more glacial become last have the model they during arrived years, have 100 to past the (McCormack innubila in adaptation Drosophila climate and migra- migration changing drive limiting the may presumably to McCormack which desert, 2005; due arid, of (Survey However, miles species diversity. of most hundreds ecological numerous for (McCormack by locations desert contains separated between of habitat tion Mexico, expanses forest leaving northwestern large retreated, by and then separated USA islands’, southwestern ‘Sky human Coe as our in how known identify located mountains to forested or archipelago, identify location, Madrean new to a 2011). populations The in Durbin human population, humans and in a a (Li utilized of population of globally frequently establishment invading spread the expansion the also ancestors between upon are and divergence fixed signatures in establishment have These increase results which the adaptation an traits population. 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Blumensteil, Caroyln Guinsberg Justin and Paul from Orive discussion Maria helpful MacDonald, with Stuart completed significant was a work showed This interest of categories functional for if Acknowledgements assess spectrum to asymptotic frequency test calculate site asymptotic to permutation synonymous asymptotic in AsymptoticMK a difference calculate and in used to used non-synonymous then We 2017) then the we Messer interval. generated which and We category, (Haller gene AsymptoticMK category. each used gene also each we category for immune results, each these sampled for confirm randomly differences To a these (Chapman and of on genes average based immune the replicates, focal finding 10000 our gene, over between background statistic 100kbp) each (within in nearby difference the calculated then We Statistic fit We multiple considering categories. immune adaptation, multiple of in estimates classed high be excessively focal to with the gene categories of a functional chromosome allowing covariates: identify gene, the to background on a GLM mutations as a of it number classed (Eilertson (Gramates total or ontologies mutations the gene effect gene using of selection FlyBase gene a Using number in each calculate gene. occurring expected for and substitutions effect mutations and these selection synonymous observed of SnIPRE and these number the non-synonymous used expected to of the also predict relative number We per to total categories sites 2011). the defined Eyre-Walker replacement account user and and into Stoletzki silent taking (McDonald 2002; model, polymorphic (DoS) (Eilertson Eyre-Walker selection and SnIPRE and of in fixed Smith direction values of 1991; specifically counts Kreitman statistics, the and McDonald-Kreitman-based used estimate We to phylogeny. gene the of our branch in polymorphic are which 005876895.1). ∼ opulation P + α eegroup Gene rmters fcategories. of rest the from tal. et .innubila D. tal. et 02,wihrfae coadKeta ae ttsisa linear a as statistics based McDonald-Kreitman reframes which 2012), +( 05 oqatf h xetta eeiieeeetcnetdiffered content element repetitive that extent the quantify to 2015) eegroup Gene ouain raesbtttoswihfie ln the along fixed which substitutions are or populations tal. et tal. et 2019). 14 ∗ 07,w otdec eeit aeoyo immune of category a into gene each sorted we 2017), opulation P )+ Chromosome tal. et 02.W acltdthe calculated We 2012). + α Chromosome n 5 confidence 95% a and 004354385.1, .innubila D. : osition P XY as α Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. 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Data may be preliminary. oee,tefeunyo Eisrin a infiatyhge neoi ein oprdt nrn and introns to compared regions exonic in assumption. higher deleterious significantly the was with insertions consistent TE 6.23e-11), Petrov of = 1989; p-value frequency Langley -6.538, the and = However, (Charlesworth t-value deleterious (GLM mildly regions least non-coding at be Muller al. to on assumed suggests et content usually This repetitive are of 0.01488). insertions accumulation = TE the p-value allowing A 19763, is element W= region Muller Test inverted of Sum A. the regions Rank element inverted in (Wilcoxon recombination the genome of in the lack densities of the insertion regions higher TE the significantly particular at at in that are than chromosome evidence TEs any one find find any not do on do though We abundant more populations. significantly other are find to orders all we compared to 1.662e-24) population = compared PR p-value to the when 11.472, related In population closely CH families 2.555e-17). 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Data may be preliminary. ttsisfrec ouain h aiasDpo otisadse iet hw0. show background to genomic line the dashed show a to contains line plot dotted D a Tajima’s has The plot Each population. each population. for each statistics for category, immune each in 4: Figure Supplementary 0. of D Tajima’s a shows line dashed grey The element. Muller the on bp) (in loci 3: Figure Supplementary ouaingntcsaitc Piws iest,Tjm’ n s)frgenes for Fst) and D Tajima’s diversity, (Pairwise statistics genetic Population aiasDb eears l ulreeet o ahpplto,lctdby located population, each for elements Muller all across gene by D Tajima’s 17 Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. hsncmaio o ahpplto,det osgicn ieecsbtencomparisons. between differences significant no to due population, each for comparison chosen B. A. 6: Figure Supplementary 5: Figure Supplementary D XY e eefrec ouain nta fsoigalpiws oprsn,w hwoerandomly one show we comparisons, pairwise all showing of Instead population. each for gene per encp ubrprpplto o ee fitrs nF in interest of genes for population per number copy Mean ihnpplto ariedvriyprgn costhe across gene per diversity pairwise population Within 18 .innubila D. ST peaks. genome. Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. oiin lososFtbtenalmlsadfmlsfo 07 ycrmsm n position. and chromosome by 2017, from females and males all between Fst shows Also position. 8: Figure Supplementary population. and population. 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Data may be preliminary. h einad9%cndneitra scluae cosalfntoa aeois hl ntespecific the in 2017). while Messer Asymptotic categories, and functional for Haller intervals all 2012; Petrov across confidence and calculated 95% (Messer than is the higher interval significantly categories confidence are functional 95% * a and ( with median test marked permutation the Categories a categories. following background for intervals the confidence 95% with teins, 10: Figure Supplementary 2017 total on 2017 and (based males frequencies 2017 allele all between minor and the Chiricahua, in 2017 and difference samples. 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TE with by colored found bars as with strain, least, each to for most content from content repetitive of up made dnie sn PopoolationTE2 using identified color). and innubila D. intronic). in non-coding, TEs region, for spectra quency 11: Figure Supplementary C. tan hw itepplto tutr.Srisaelble yterpplto bt shape (both population their by labelled are Strains structure. population little shows strains enT neto est e M idw(ldn M)frec ouainof population each for 1Mb) (sliding window 1Mb per density insertion TE Mean .innubila D. B. h rnpsbeeeetcnetof content element transposable The rnil opnn nlss(hwn C )o Eisrin across insertions TE of 2) & 1 PCs (showing analysis component Principle . Eisrin r ooe yterorder. their by colored are insertions TE eaae yT re n h oaino neto eg coding (e.g. insertion of location the and order TE by separated 21 rspiainnubila Drosophila D. rprino h genome the of Proportion . A. neto fre- Insertion .innubila, D. Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. upeetr al 4: Table Supplementary functions. and components processes, by 3: Table Supplementary population. each for eachbackground for accessions 2: Table SRA contains Supplementary Also autosomes. chromosome, X for strain. coverage of summary including study, 1: Table Supplementary L o ouaingntcsaitc nimn eectgre eaiet the to relative categories gene immune in statistics genetic population for GLM umr fGMfreeae coadKita ttsisG aeoisin categories GO statistics McDonald-Krietman elevated for GLM of Summary umr fgn nooyercmnsfrF for enrichments ontology gene of Summary umr of Summary rspiainnubila Drosophila 22 ysDAcletdadsqecdfrthis for sequenced and collected DNA fly’s ST nec ouain separated population, each in Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. n h ffcso igencetd oyopim,Spff Nsi h eoeo rspiamelanogaster Drosophila of genome the in 6 SNPs Fly SnpEff: iso-3. polymorphisms, iso-2; nucleotide w1118; single Nguyen strain T. of Coon, effects M. the Wang, L. ing 32 L. Bioinformatics Platts, A. Schlesinger applications. P., sequencing F. Cingolani, cancer Barnes, and germline B. for indels Shaw, and R. variants Schulz-Trieglaff, structural O. X., in Chen, distributions element Transposable 1997 147 Sniegowski, D. Genetics P. of and . genetics Langley H. population C. B., The Charlesworth, 1989 23 Langley, genetics of H. review 34 C. Structure Annual Systematics Geographic and and and Evolution, B., Genetic Ecology, of Charlesworth, of Effects Review The 2003 Annual Barton, Variation. H. Neutral N. variation on and genetic Charlesworth of D. maintenance drives B., selection Charlesworth, Balancing 2019 Unckless, L. variation R. genetic and in hidden Hill Extensive T. 2017 R., J. Emerson, in Chapman, J. elements J. functional and of Kalsow structure S. the Zhang, shapes X. Zhao, Conflict. R. in M., Genes Chakraborty, in 2006 Trivers, variation R. Seasonal and 2015 A., Schmidt, Burt, S. P. and Heschel 2018 M. V., S. Buffalo, O’Brien, two R. in K. traits Watson, history S. eukaryoticlife S. in elements Canadian L., repetitive E. of migration. database Behrman, a mammal Update, 6 of Repbase 2015 DNA benefits Kohany, Mobile O. adaptive and genomes. the Kojima K. On K. W., 2014 Bao, Fryxell, M. 92 J. Zoology and of invasive Street, Journal the of G. phylogeography T., and variability Avgar, Genetic 2005 in Powell, E. and pp. mussel, Wilson Fire, zebra J. 2 Gosling, National E. Horseshoe Chiricahua I., 2011 Astanei, the the to of Trip Magazine. Impacts Field Geology the Consortium Arizona of Science 6 Discussion Fire Microbiology Southwest in Monument: Frontiers 2012 species. L., invasive global Arechederra-Romero, 2015 tool. Vasconcelos, a search M. of alignment V. ecophysiology local and and Basic phylogeography, Leao 1990 bution, N. Lipman, P. J. T., D. J. and Antunes, Myers 215 W. Biology E. Molecular Miller, of W. Gish, Journal W. F., S. Altschul, Bibliography population. each for SnIPRE 3: Data Supplementary population. each for VCFtools 2: Data Supplementary GWAS. in and statistics 1: Data Supplementary 5: Table Supplementary innubila D. Drosophila . risn oyopa(Pallas) polymorpha Dreissena niirba etds eoeBooyadEouin11 Evolution and Biology Genome peptides. antimicrobial : 1993-1995. Scythe : 481-490. Drosophila : . 4-9. umr fgn nooyercmnsfrD for enrichments ontology gene of Summary : C l o Nsin SNPs for file VCF coadKeta ttsiscluae o ahgn in gene each for calculated statistics McDonald-Kreitman ouaingntcsaitc acltdfrec eein gene each for calculated statistics genetic Population 251-287. : : 80-92. 403-410. pce.Junlo vltoayBooy28 Biology Evolutionary of Journal species. o cl14 Ecol Mol . Drosophila .innubila D. 23 yidoprossraciborskii: Cylindrospermopsis tal. et o.r 50 Doi.Org . : 1655-1666. 02Apormfranttn n predict- and annotating for program A 2012 , sdi siaino ouaingenetic population of estimation in used , tal. et : : 114967. 2691-2701. Drosophila 06Mna ai eeto of detection Rapid Manta: 2016 , XY nec population. each in rzn elg Magazine Geology Arizona : 1691-1704. : 99-125. rnpsbeelements. transposable eiwo h distri- the of review .innubila D. .innubila D. : Drosophila 1220-1222. : 473. using using , Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. ulr .L,G .Hye,S ihrsadS .Shee,21 eoiso aua ouain:How Populations: Natural of Genomics Genetics. 2016 in. Schaeffer, Inversions W. Chromosomal of S. Evolution and the Richards of Shape S. estimation Genes Haynes, efficient Expressed D. and Differentially G. Fast Fran¸cois, L., 2014 O. Z. Fuller, and Bouchard 196 Genetics G. coefficients. Trouillon, ancestry T. individual 164 Mathieu, Genetics F. genotype frequencies. E., multilocus Frichot, allele using of structure correlated population Review and of Annual Inference loci 2003 Linked Pritchard, Expansions. K. data: Range J. and Poisson of Stephens Consequences a M. D., Genetic Using Falush, 2009 Inference 40 Petit, Selection Systematics J. and SnIPRE: R. Evolution, and 2012 Ecology, Foll Bustamante, M. D. L., 8. C. Biology Excoffier, Computational and PLoS in Booth male-killing Model. G. embryonic Effects J. Random of E., modulation K. and Eilertson, Expression 2005 Jaenike, J. 59 and evolution Minhas S. innubila M. Drosophila A., K. association: host-parasite Dyer, structured spatially a of dynamics 1518-1528. Evolutionary 2005 Jaenike, innubila J. Drosophila 168 and Genetics in a., Genomes. Endosymbiont K. Parasite Male-Killing Dyer, and a Host by the Infection From Stable Evidence of Evolutionarily Molecular response 2004 antiviral A., Galiana-Arnoux the natural K. for D. Dyer, of sufficient Troxler, not Genetics L. but Irving, 1963 required P. Wallace, is Jouanguy, pathway B. E. and C., Spassky Dostert, of B. population Pavlovsky, marginal O. isolated an Hunter, 91-103. of Genetics S. XXXI. A. populations. H., of T. Chromosomes Dobzhansky, In Inversions 1937 Sturtevant, Deleterious 23 H. and netics A. Heterotic XL: and Populations T., of Natural Dobzhansky, Populations of in Genetics Lethals The Recessive 1968 43 of Spassky, genetics Effects B. Nature and Maguire data. T., R. sequencing Dobzhansky, J. DNA Garimella, next-generation V. using K. genotyping Poplin, Banks R. and discovery Banks, E. E. Albers, A., M. A. DePristo, C. Abecasis, 27 disparity G. Bioinformatics the Auton, unifying VCFtools. 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Wolbachia : 481-501. : rspiapseudoobscura Drosophila 973-983. vlto;itrainljunlo rai vlto 59 evolution organic of journal international Evolution; . 24 : 3133-3157. : tal. et 1567-1587. Drosophila. rspiasuzukii Drosophila rspiapseudoobscura Drosophila tal. et tal. et 01Tevratcl omtand format call variant The 2011 , : eeis59 Genetics . 1443-1455. 01Afaeokfrvariation for framework A 2011 , 05TeJkSA signaling Jak-STAT The 2005 , : rspiapseudoobscura. Drosophila 149-160. a muo 6 Immunol Nat : nErp n draft a and Europe in rspiainnubila Drosophila 411-425. : 491-498. eeis48 Genetics . : 946-953. Ge- : : : : Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. fsiolsaidcdml iln nDoohl eaoatr eeiy(dn)102 (Edinb) expression the Heredity against melanogaster. genotype Drosophila host of in files. Effects killing fastQ 2009 Fukatsu, male for T. spiroplasma-induced and tool of Shimada trimming M. Anbutsu, quality-based H. adaptive, D., window, Kageyama, sliding A Sickle: 2011 Fass, 1.33. J. and N., Joshi, 21 male-killing to Biology resistance Evolutionary No of 2008 Dyer, Journal while A. K. sweeps and selective J., SE) Jaenike, Reyolds recent J., Detecting Rolff 2009 2016 (eds Elftherianos, immunity Nielsen, and I. 25 R. and Ecol Mol J., and selection. Imler, Hellmann background and I. rate DeGiorgio, mutation for M. controlling D., C. Huber, Partridge C. T. Lundblad, Http://broadinstitute.github.io/picard, K. Reviews Science Cooper, Quaternary Africa. J. Southern in R. years 25,000 22 G. past the over Lee-Thorp, variability climatic A. millennial-scale J. of K., response 188 Holmgren, immune Nat The Am 2003 Directions. A., Future Bradburd J. and G. virus. Hoffmann, Solutions, Antolin, DNA F. Practical insect M. Pitfalls, Lotterhos, an Adaptation: E. 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Wolbachia tal. et : 1243-1254. rspiainnubila Drosophila tal. et .Gnm ilg n vlto 7 Evolution and Biology Genome ). 05D ooasml n annotation and assembly novo De 2015 , : tal. et 142-156. 00Nwagrtm n methods and algorithms New 2010 , fe huad fyaso infection. of years of thousands after : : 1-36. 33-38. 06FnigteGnmcBasis Genomic the Finding 2016 , : 907-913. tal. et tal. et eel lineage-specific reveals 07Fyaea 25: at FlyBase 2017 , : : 379-397. 475-482. 03Persistent 2003 , : 1192- Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. az,M,M ugadA uz 08TeFlbc-ieeeetGlloblnst h uefml of of superfamily Academy P National the the to of Proceedings belongs genus. Galileo Drosophila element Foldback-like the The within widespread 2008 is Ruiz, and A. transposons and Technical DNA Puig reads. M. sequencing M., high-throughput Marzo, from sequences adapter removes Cutadapt Notes 2011 M., Martin, akw .A,adP ’rd,2006 O’Grady, P. and A., T. Markow, of Populations Natural in Fecundity Genetics Affecting . Loads Ayroles Genetic F. 1967 J. D., Marinkovic, Barbadilla, A. Stone, a. E. Richards, gaster S. C., F. T. Mackay, n/a. ahd,H . .O egad .R ’re,E .Bhmn .S Schmidt S. P. Behrman, L. E. O’Brien, in R. variation K. latitudinal of Bergland, fixed genomics O. of population A. effects of E., extent H. in genomic Machado, flow the of gene Evaluation interspecific 2007 and Noor, persimilis variation F. Drosophila a. intraspecific M. on and differences Haselkorn inversion S. T. ( a., C. Orangutans Machado, of History new Degenhardt Demographic 8. D. ideas, and ONE J. old PLoS Speciation Musharoff, evolution: S. Rich DNA Eilertson, Satellite a K. 2018 Kelley, Reveals Barbash, L. A. J. X., D. Ma, and 49 Clark Dev G. Genet A. Opin McGurk, Curr P. genetics approaches. M. 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Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. akn .A,adJ .A ucse,19 h oto irto nIscs nulRve fEntymology of Review Annual Insects. in Migration of Cost The 1992 Burchsted, modern albopictus. A. a C. Aedes 37 J. of mosquito and history A., tiger Glacial M. Asian Rankin, 2012 the Urbanelli, of S. 7 modelling and One distribution Somboon PLoS species P. and Bellini, phylogeography R. invader: Mastrantonio, V. D., Porretta, Cardeno M. C. Stevens, 1-24. A. K. Sugino, P. Sub-Saharan R. of Corbett-detig, B. of R. E., DPGP3. genomics J. 2013 Pool, Population Langley, Gonz´alez, 2011 H. J. C. and and J., Lenkov Pool, K. Lipatov, natural M. across in Fiston-Lavier, elements impacts A.-S. transposable change climate a., of D. fingerprint Petrov, coherent globally A 421 2003 Nature Yohe, systems. 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LSOE6 ONE PLoS . 28 nIead o cl22 Ecol Mol Ireland. in ) : 353-357. : tal. et : 1-6. : tal. et 63-82. 937-954. : 02DLY tutrlvratdiscovery variant structural DELLY: 2012 , 4287-4294. tal. et 08Atiuigpyia n biological and physical Attributing 2008 , : tal. et : e26564. i333-i339. Wolbachia Drosophila 2011 , 09TeCli rneo Britain: of fringe Celtic The 2009 , tal. et : rspiasuzukii Drosophila 2971-2985. 05Gn e enrichment set Gene 2005 , in : 678-689. aue415 Nature . rspiainnubila Drosophila : 1022-1024. (Diptera: : : 15545– 1-14. By Posted on Authorea 17 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159242077.72607009 — This a preprint and has not been peer reviewed. Data may be preliminary. abn .A,M adkmr .N ahraadL .W,20 h olptwyi motn o an for important is pathway Toll The 2005 Wu, P. L. and Vakharia detect N. in to V. 25 response approach Nandakumar, Bioinformatics antiviral growth M. reads. pattern A., short a R. paired-end : Zambon, from Pindel insertions 2009 sized Ning, medium Z. and and deletions Apweiler 2865-2871. large R. of Long, points Q. Schulz, break H. M. populations K., natural Ye, in structure haplotype and Subdivision 2003 Charlesworth, D. of and Lauga B. I., S. Wright, rbdpi lyrata Arabidopsis Drosophila oeua clg 12 Ecology Molecular . rceig fteNtoa cdm fSine 102 Sciences of Academy National the of Proceedings . : 1247–1263. 29 : 7257-7262. :