Philippa Kaur

Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, DenmarkPatrick Munk, Christian Brinch, Frederik Duus Møller, Thomas N. Petersen, Rene S. Hendriksen, Anne Mette Seyfarth, Jette S. Kjeldgaard, Christina Aaby Svendsen & Frank M. AarestrupCentre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UKBram van Bunnik & Mark WoolhouseCentre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, SwedenFanny Berglund & D. G. Joakim LarssonDepartment of Viroscience, Erasmus MC, Rotterdam, The NetherlandsMarion KoopmansInstitute of Public Health, Tirana, AlbaniaArtan BegoUniversidad de Buenos Aires, Buenos Aires, ArgentinaPablo PowerMelbourne Water Corporation, Melbourne, AustraliaCatherine Rees & Kris CoventryCharles Darwin University, Darwin, AustraliaDionisia LambrinidisUniversity of Copenhagen, Frederiksberg C, DenmarkElizabeth Heather Jakobsen Neilson & Yaovi Mahuton Gildas HounmanouCharles Darwin University, Darwin Northern Territory, AustraliaKaren GibbCanberra Hospital, Canberra, AustraliaPeter CollignonALS Water, Scoresby, AustraliaSusan CassarAustrian Agency for Health and Food Safety (AGES), Vienna, AustriaFranz AllerbergerUniversity of Dhaka, Dhaka, BangladeshAnowara Begum & Zenat Zebin HossainEnvironmental Protection Department, Bridgetown, St. Michael, BarbadosCarlon WorrellLaboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Brussels, BelgiumOlivier VandenbergAQUAFIN NV, Aartselaar, BelgiumIlse PietersPolytechnic School of Abomey-Calavi, Abomey-Calavi, BeninDougnon Tamègnon VictorienUniversidad Catσlica Boliviana San Pablo, La Paz, BoliviaAngela Daniela Salazar Gutierrez & Freddy SoriaPublic Health Institute of the Republic of Srpska, Faculty of Medicine University of Banja Luka, Banja Luka, Bosnia and HerzegovinaVesna Rudić GrujićPublic Health Institute of the Republic of Srpska, Banja Luka, Bosnia and HerzegovinaNataša MazalicaBotswana International University of Science and Technology, Palapye, BotswanaTeddie O. RahubeUniversidade Federal de Minas Gerais, Belo Horizonte, BrazilCarlos Alberto Tagliati & Larissa Camila Ribeiro de SouzaOswaldo Cruz Institute, Rio de Janeiro, BrazilDalia RodriguesVale Institute of Technology, Belιm, PA, BrazilGuilherme OliveiraNational Center of Infectious and Parasitic Diseases, Sofia, BulgariaIvan IvanovUniversity of Ouagadougou, Ouagadougou, Burkina FasoBonkoungou Isidore Juste & Traoré OumarInstitut Pasteur du Cambodge, Phnom Penh, CambodiaThet Sopheak & Yith VuthyCentre Pasteur du Cameroun, Yaoundι, CameroonAntoinette Ngandjio, Ariane Nzouankeu & Ziem A. Abah Jacques OlivierUniversity of Regina, Regina, CanadaChristopher K. YostEau Terre Environnement Research Centre (INRS-ETE), Quebec City G1K 9A9, Canada and Indian Institute of Technology, Jammu, IndiaPratik KumarEau Terre Environnement Research Centre (INRS-ETE), Quebec City G1K 9A9, Canada and Lassonde School of Enginerring, York University, Toronto, CanadaSatinder Kaur BrarUniversity of N’Djamena, N’Djamena, ChadDjim-Adjim TaboEscuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, ChileAiko D. AdellInstitute of Public Health, Santiago, ChileEsteban Paredes-Osses & Maria Cristina MartinezUniversidad Catolica del Maule, Centro de Biotecnología de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, ChileSara Cuadros-OrellanaGuangdong Provincial Center for Disease Control and Prevention, Guangzhou, ChinaChangwen Ke, Huanying Zheng & Li BaishengThe Hong Kong Polytechnic University, Hong Kong, ChinaLok Ting Lau & Teresa ChungShantou University Medical College, Shantou, ChinaXiaoyang JiaoNanjing University of Information Science and Technology, Nanjing, ChinaYongjie YuCenter for Disease Control and Prevention of Henan province, Zhengzhou, ChinaZhao JiaYongColombian Integrated Program for Antimicrobial Resistance Surveillance – Coipars, CI Tibaitatα, Corporaciσn Colombiana de Investigaciσn Agropecuaria (AGROSAVIA), Tibaitatα – Mosquera, Cundinamarca, ColombiaJohan F. Bernal Morales, Maria Fernanda Valencia & Pilar Donado-GodoyInstitut Pasteur de Côte d’Ivoire, Abidjan, Côte d’IvoireKalpy Julien CoulibalyUniversity of Zagreb, Zagreb, CroatiaJasna HrenovicAndrija Stampar Teaching Institute of Public Health, Zagreb, CroatiaMatijana JergovićVeterinary Research Institute, Brno, Czech RepublicRenáta KarpíškováCentre de Recherche en Sciences Naturelles de Lwiro (CRSN-LWIRO), Bukavu, Democratic Republic of CongoZozo Nyarukweba DeogratiasBIOFOS A/S, Copenhagen K, DenmarkBodil ElsborgTechnical University of Denmark, Kgs., Lyngby, DenmarkLisbeth Truelstrup Hansen & Pernille Erland JensenSuez Canal University, Ismailia, EgyptMohamed AbouelnagaUniversity of Sadat City, Sadat City, EgyptMohamed Fathy SalemMinistry of Health, Environmental Microbiology, Tallinn, EstoniaMarliin KoolmeisterAddis Ababa University, Addis Ababa, EthiopiaMengistu Legesse & Tadesse EgualeUniversity of Helsinki, Helsinki, FinlandAnnamari HeikinheimoFrench Institute Search Pour L’exploitation De La Mer (Ifremer), Nantes, FranceSoizick Le Guyader & Julien SchaefferInstituto Nacional de Investigaciσn en Salud Pϊblica-INSPI (CRNRAM), Galαpagos, Quito, EcuadorJose Eduardo VillacisNational Public Health Laboratories, Ministry of Health and Social Welfare, Kotu, GambiaBakary SannehNational Center for Disease Control and Public Health, Tbilisi, GeorgiaLile MalaniaRobert Koch Institute, Berlin, GermanyAndreas Nitsche & Annika BrinkmannTechnische Universitδt Dresden, Institute of Hydrobiology, Dresden, GermanySara Schubert, Sina Hesse & Thomas U. BerendonkUniversity for Development Studies, Tamale, GhanaCourage Kosi Setsoafia SabaUniversity of Ghana, Accra, GhanaJibril MohammedKwame Nkrumah University of Science and Technology, Kumasi, PMB, GhanaPatrick Kwame FegloCouncil for Scientific and Industrial Research Water Research Institute, Accra, GhanaRegina Ama BanuVeterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Thermi, GreeceCharalampos KotzamanidisAthens Water Supply and Sewerage Company (EYDAP S.A.), Athens, GreeceEfthymios LytrasUniversidad de San Carlos de Guatemala, Guatemala City, GuatemalaSergio A. LickesSemmelweis University, Institute of Medical Microbiology, Budapest, HungaryBela KocsisUniversity of Veterinary Medicine, Budapest, HungaryNorbert SolymosiUniversity of Iceland, Reykjavνk, IcelandThorunn R. ThorsteinsdottirCochin University of Science and Technology, Cochin, IndiaAbdulla Mohamed HathaKasturba Medical College, Manipal, IndiaMamatha BallalApollo Diagnostics, Mangalore, IndiaSohan Rodney BangeraShiraz University of Medical Sciences, Shiraz, IranFereshteh FaniShahid Beheshti University of Medical Sciences, Tehran, IranMasoud AlebouyehNational University of Ireland Galway, Galway, IrelandDearbhaile Morris, Louise O’Connor & Martin CormicanBen Gurion University of the Negev and Ministry of Health, Beer-Sheva, IsraelJacob Moran-GiladIstituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, ItalyAntonio Battisti, Elena Lavinia Diaconu & Patricia AlbaCNR – Water Research Institute, Verbania, ItalyGianluca Corno & Andrea Di CesareNational Institute of Infectious Diseases, Tokyo, JapanJunzo Hisatsune, Liansheng Yu, Makoto Kuroda, Motoyuki Sugai & Shizuo KayamaNational Center of Expertise, Taldykorgan, KazakhstanZeinegul ShakenovaMount Kenya University, Thika, KenyaCiira KiiyukiaKenya Medical Research Institute, Nairobi, KenyaEric Ng’enoUniversity of Prishtina “Hasan Prishtina” & National Institute of Public Health of Kosovo, Pristina, KosovoLul RakaKuwait Institute for Scientific Research, Kuwait City, KuwaitKazi Jamil, Saja Adel Fakhraldeen & Tareq AlaatiInstitute of Food Safety, Riga, LatviaAivars Bērziņš, Jeļena Avsejenko, Kristina Kokina, Madara Streikisa & Vadims BartkevicsAmerican University of Beirut, Beirut, LebanonGhassan M. MatarCentral Michigan University & Michigan Health Clinics, Saginaw, MI, USAZiad DaoudNational Food and Veterinary Risk Assessment Institute, Vilnius, LithuaniaAsta Pereckienė & Ceslova Butrimaite-AmbrozevicieneLuxembourg Institute of Science and Technology, Belvaux, LuxembourgChristian PennyInstitut Pasteur de Madagascar, Antananarivo, MadagascarAlexandra Bastaraud & Jean-Marc CollardUniversity of Antananarivo, Centre d’Infectiologie Charles Mιrieux, Antananarivo, MadagascarTiavina Rasolofoarison, Luc Hervé Samison & Mala Rakoto AndrianariveloUniversity of Malawi, Blantyre, MalawiDaniel Lawadi BandaMalaysian Genomics Resource Centre Berhad, Kuala Lumpur, MalaysiaArshana AminAIMST University, COMBio, Kedah, MalaysiaHeraa Rajandas & Sivachandran ParimannanWater Services Corporation, Luqa, MaltaDavid SpiteriEnvironmental Health Directorate, St. Venera, MaltaMalcolm Vella HaberUniversity of Mauritius, Reduit, MauritiusSunita J. SantchurnInstitute for Public Health Montenegro, Podgorica, MontenegroAleksandar Vujacic & Dijana DjurovicInstitut Pasteur du Maroc, Casablanca, MoroccoBrahim Bouchrif & Bouchra KarraouanCentro de Investigaηγo em Saϊde de Manhiηa (CISM), Maputo, MozambiqueDelfino Carlos VubilAgriculture and Forestry University, Kathmandu, NepalPushkar PalNational Institute for Public, Health and the Environment (RIVM), Bilthoven, The NetherlandsHeike Schmitt & Mark van PasselUniversity of Otago, Dunedin, New ZealandGert-Jan Jeunen & Neil GemmellUniversity of Otago, Christchurch, New ZealandStephen T. ChambersUniversity of Central America, Managua, NicaraguaFania Perez Mendoza & Jorge Huete-PιrezUniversidad Nacional Autσnoma de Nicaragua-Leσn, Leσn, NicaraguaSamuel VilchezUniversity of Ilorin, Ilorin, NigeriaAkeem Olayiwola Ahmed, Ibrahim Raufu Adisa & Ismail Ayoade OdetokunUniversity of Ibadan, Ibadan, NigeriaKayode FashaeNorwegian Institute of Public Health, Oslo, NorwayAnne-Marie Sørgaard & Astrid Louise WesterVEAS, Slemmestad, NorwayPia Ryrfors & Rune HolmstadUniversity of Agriculture, Faisalabad, PakistanMashkoor MohsinAga Khan University, Karachi, PakistanRumina Hasan & Sadia ShakoorLaboratorio Central de Salud Publica, Asuncion, ParaguayNatalie Weiler Gustafson & Claudia Huber SchillInstituto Nacional de Salud, Lima, PeruMaria Luz Zamudio RojasUniversidad de Piura, Piura, PeruJorge Echevarria Velasquez & Felipe Campos YauceWHO Environmental and Occupational Health, Manila, PhilippinesBonifacio B. MagtibayMaynilad Water Services, Inc., Quezon City, PhilippinesKris Catangcatang & Ruby SibuloNational Veterinary Research Institute, Pulawy, PolandDariusz WasylUniversidade Catσlica Portuguesa, CBQF – Centro de Biotecnologia e Quνmica Fina – Laboratσrio Associado, Escola Superior de Biotecnologia, Porto, PortugalCelia Manaia & Jaqueline RochaAguas do Tejo Atlantico, Lisboa, PortugalJose Martins & Pedro ÁlvaroGwangju Institute of Science and Technology, Gwangju, Republic of KoreaDoris Di Yoong Wen, Hanseob Shin & Hor-Gil HurKorea Advanced Institute of Science and Technology, Daejeon, Republic of KoreaSukhwan YoonInstitute of Public Health of the Republic of North Macedonia, Skopje, Republic of North MacedoniaGolubinka Bosevska & Mihail KochubovskiState Medical and Pharmaceutical University, Chișinău, Republic of MoldovaRadu CojocaruNational Agency for Public Health, Chișinău, Republic of MoldovaOlga BurduniucKing Abdullah University of Science and Technology, Thuwal, Saudi ArabiaPei-Ying HongUniversity of Edinburgh, Edinburgh, Scotland, UKMeghan Rose PerryInstitut Pasteur de Dakar, Dakar, SenegalAmy GassamaInstitute of Veterinary Medicine of Serbia, Belgrade, SerbiaVladimir RadosavljevicNanyang Technological University, Singapore, SingaporeMoon Y. F. Tay, Rogelio Zuniga-Montanez & Stefan WuertzPublic Health Authority of the Slovak Republic, Bratislava, SlovakiaDagmar Gavačová, Katarína Pastuchová & Peter TruskaNational Laboratory of Health, Environment and Food, Ljubljana, SloveniaMarija TrkovIndependent consultant, Johannesburg, South AfricaKaren KeddyDaspoort Waste Water Treatment Works, Pretoria, South AfricaKerneels EsterhuyseKorea Advanced Institute of Science and Technology, Daejeon, South KoreaMin Joon SongSchool of Veterinary Sciences, Lugo, SpainMarcos Quintela-BalujaLabaqua, Santiago de Compostela, SpainMariano Gomez LopezIRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autonoma de Barcelona, Bellaterra, SpainMarta Cerdà-CuéllarUniversity of Kelaniya, Ragama, Sri LankaR. R. D. P. Perera, N. K. B. K. R. G. W. Bandara & H. I. PremasiriMedical Research Institute, Colombo, Sri LankaSujatha PathirageCaribbean Public Health Agency, Catries, Saint LuciaKareem CharlemagneThe Sahlgrenska Academy at the University of Gothenburg, Gothenburg, SwedenCarolin RutgerssonSwedish University of Agricultural Sciences, Uppsala, SwedenLeif Norrgren & Stefan ÖrnFederal Food Safety and Veterinary Office (FSVO), Bern, SwitzerlandRenate BossAra Region Bern AG, Herrenschwanden, SwitzerlandTanja Van der HeijdenCenters for Disease Control, Taipei, TaiwanYu-Ping HongKilimanjaro Clinical Research Institute, Moshi, TanzaniaHappiness Houka KumburuSokoine University of Agriculture, Morogoro, TanzaniaRobinson Hammerthon MdegelaFaculty of Science and Technology, Suratthani Rajabhat University, Surat Thani, ThailandKaknokrat ChonsinFaculty of Public Health, Mahidol University, Bangkok, ThailandOrasa SuthienkulFaculty of Medicine Siriraj Hospital, Bangkok, ThailandVisanu ThamlikitkulNational Institute for Public Health and the Environment (RIVM), Bilthoven, NetherlandsAna Maria de Roda HusmanNational Institute of Hygiene, Lomι, TogoBawimodom BidjadaAgence de Mιdecine Prιventive, Dapaong, TogoBerthe-Marie Njanpop-LafourcadeDivision of Integrated Surveillance of Health Emergencies and Response, Lomι, TogoSomtinda Christelle Nikiema-PessinabaPublic Health Institution of Turkey, Ankara, TurkeyBelkis LeventHatay Mustafa Kemal University, Hatay, TurkeyCemil KurekciMakerere University, Kampala, UgandaFrancis Ejobi & John Bosco KaluleAbu Dhabi Public Health Center, Abu Dhai, United Arab EmiratesJens ThomsenDubai municipality, WWTP Al Aweer, Dubai, UAEOuidiane ObaidiRashid Hospital, Dubai, UAELaila Mohamed JassimNorthumbrian Water, Northumbria House, Abbey Road, Pity Me, Durham, UKAndrew MooreUniversity of Exeter Medical School, Cornwall, UKAnne Leonard, Lihong Zhang & William H. GazeNewcastle University, Newcastle upon Tyne, UKDavid W. Graham & Joshua T. BunceBrightwater Treatment Plant, Woodinville, WA, USABrett LeforDepartment of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USADrew Capone & Joe BrownUniversity of North Carolina, Chapel Hill, USAEmanuele Sozzi & Mark D. SobseyUniversity of Washington, Seattle, WA, USAJohn Scott Meschke, Nicola Koren Beck, Pardi Sukapanpatharam & Phuong TruongBaylor University, Waco, USAMichael DavisColumbia Boulevard WWTP, Portland, USARonald LilienthalEastern Illinois University, Charleston, USASanghoon KangThe Ohio State University, Columbus Ohio, USAThomas E. WittumLaboratorio Tecnolσgico del Uruguay, Montevideo, UruguayNatalia Rigamonti & Patricia BaklayanInstitute of Public Health in Ho Chi Minh City, Ho Chi Minh, VietnamChinh Dang Van, Doan Minh Nguyen Tran & Nguyen Do PhucUniversity of Zambia, Lusaka, ZambiaGeoffrey Kwenda More

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Institute of Carbon Neutrality, Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, ChinaQian Zhao, Yao Zhang & Shilong PiaoSchool of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, ChinaZaichun Zhu & Hui ZengKey Laboratory of Earth Surface System and Human—Earth Relations, Ministry of Natural Resources of China, Shenzhen Graduate School, Peking University, Shenzhen, ChinaZaichun Zhu & Hui ZengDepartment of Earth and Environment, Boston University, Boston, MA, USARanga B. MyneniCSIC, Global Ecology Unit CREAF-CSIC-UAB, Barcelona, Catalonia, SpainJosep PeñuelasCREAF, Barcelona, Catalonia, SpainJosep PeñuelasState Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, ChinaShilong Piao More

Ethics statementAnimals’ care was in accordance with institutional guidelines. Ethical permit was issued by Malmö-Lund djurförsöksetiska nämnd 5.8.18-00848/2018.Field workWe carried out the field work in Sweden during four breeding seasons (2018–2021). Adult male willow warblers were captured in their breeding territories using mist nets and playback of a song. From each bird, we collected the innermost primary feather from the right wing. From the birds that returned with a logger we also collected ~20 μl of blood from the brachial wing vein. The blood was stored in SET buffer (0.015 M NaCl, 0.05 M Tris, 0.001 M of EDTA, pH 8.0) at room temperature until deposited for permanent storage at −20 °C. We deployed Migrate Technology Ltd geolocators (Intigeo-W30Z11-DIP 12 × 5 × 4 mm, 0.32 g) and used a nylon string to mount them on birds with the “leg-loop” harness method as outlined in our previous work24. The mass of the logger relative to that of the bird was on average 3.3% (range 2.7–3.8%).The tagged birds were ringed with a numbered aluminum ring, and two, colored plastic rings for later identification in the field. In total, we tagged 466 males (349 in 2018 and 117 in 2020) at breeding territories. During the first tagging season (2018), birds were trapped at 17 locations (average 22 birds per site; range 7–30) distributed across Sweden (Fig. S1). Three of the sites were in southern Sweden to document migration routes of allopatric trochilus and three sites were located above the Arctic circle to record migratory routes of allopatric acredula, whereas the remaining (239) loggers were spread over 11 sites located in the migratory divide. Given the observed densities and distribution of hybrids after analyzing returning birds in 2019, we deployed 117 more loggers at one single site (63.439°N, 14.831°E) in 2020. We successfully retrieved tracks from 57 birds tagged in 2019 and 16 from birds tagged in 2021. In search for birds with loggers, we checked circa 3000 willow warbler males and covered an area of at least 0.5 km radius around each site the year after tagging.Geolocator data treatmentThe R package GeoLight (version 2.0)25 was used to extract and analyze locations from raw geolocator data. All twilight events were obtained with light threshold of 3 lux. The most extreme outliers were trimmed with “loessFilter” function and a K value of 3. We used GeoLight’s function “getElevation” for estimating the sun elevation angle for the breeding period: these sets of locations were used to infer the positions for autumn departure direction. In addition, we carried out a “Hill-Ekström” calibration for the longest stationary winter site during the period before the spring equinox. Winter calibration produced location sets that better reflected the winter coordinates of the main winter site in sub-Saharan Africa26. We reduced some of the inherent geolocation “noise” by applying cantered 5-day rolling means to the coordinates. The equinox periods were visually identified by inspecting standard deviations in latitude. Latitudes from equinox periods were omitted (on average autumn equinox obscured data for 45 days (range 25–68). For the main winter site, we used the longest period at which bird stayed stationary and from which in all cases begun the spring migration (mean = 118, SD = 23 days). Timing of autumn departure was estimated by manual inspection of longitudes and latitudes plotted in time series. To estimate at which longitude the birds crossed the Mediterranean, we extracted the longitude when birds crossed latitude 35 N° (Mediterranean crossing longitude). For 29 birds, it was possible to directly extract the longitude at crossing latitude 35 N°. For the rest of the cases, the birds had not reached latitude 35 N° before the latitude was obscured by the equinox, we calculated the mean longitude of 10 days from the onset of fall equinox as a measure of the Mediterranean crossing. This measurement correlated highly with the winter longitude (r = 0.78, p = 2.8 × 10−16). To control for the birds relative breeding site longitude, we extracted the departure direction (1°–360°) relative from the tagging site to the location where the birds crossed the Mediterranean (departure direction). The departure data was of circular type (measured in 360°), however the variance did not span more than 180° degrees (range 151°–224°). Therefore, we proceeded with analyses using linear statistics. Geographic distances and departure direction were calculated using R package “geosphere” (version 1.5-10). Complete set of positions of each individual bird with equinoxes excluded is presented in Supplementary Data 1.Laboratory work and molecular data extractionWe extracted DNA from blood samples following the ammonium acetate protocol16. Genotyping for divergent regions on chromosome 1 (InvP-Ch1) and chromosome 5 (InvP-Ch5) was done using a qPCR SNP assay16, which is based on one informative SNP per region (SNP 65 for chromosome 1 and SNP 285 for chromosome 5). Probes and primers were produced by Thermo Fisher Scientific and were designed using the online Custom TaqMan® Assay Design tool (Table S4). We used Bio-Rad CFX96™ Real-time PCR system (Bio-Rad Laboratories, CA, USA) and the universal Fast-two-steps protocol: 95 °C, 15 min—40*(95 °C, 10 s–60 °C, 30 s, plate read. Both regions contain inversion polymorphisms that restrict recombination between subspecies-specific haplotypes and contain nearly all the SNPs separating the two subspecies13. For each region, we scored genotypes as either “Tro” (homozygous for trochilus haplotypes), “Acr” (homozygous for acredula haplotypes) or “Het” (heterozygous). The method that we used to assess the presence of MARB-a is based on a qPCR assay that quantifies the copy number of a novel TE (previously known as AFLP-WW212) that has expanded in acredula. The quantification of repeats by this method has been shown to be highly repeatable (R2 = 0.88) when comparing estimates obtained from DNA in blood and feathers15. We used the forward (5′-CCTTGCATACTTCTATTTCTCCC-3′) and reverse (5′-CATAGGACAGACATTGTTGAGG-3′) primers developed by Caballero-López et al.15 to amplify the TE motif. For reference of a single copy region we used the primers SFRS3F and SFRS3R27. We diluted DNA to 1 ng/μl−1 and used a Bio-Rad CFX96™ Real-time PCR system (Bio-Rad Laboratories, CA, USA) with SYBR-green-based detection. Total reaction volume was 25 μl of which 4 μl of DNA, 12.5 μl of SuperMix, 0.1 μl ROX, 1 μl of primer (forward and reverse), and 6.4 μl of double distilled H2O. We ran quantifications of the single copy gene and the TE variant found on MARB-a on separate plates with the following settings: 50 °C for 2 min as initial incubation, 95 °C for 2 min X 43 (94 °C for 30 s [55.3 °C SFRS3 and 55.5 °C for TE, 30 s] and 72 °C for 45 s). Each sample was run in duplicate and together with a two-fold serial standard dilution (2.5–7.8 × 10−2 ng). Allopatric trochilus have 0–6 copies whereas allopatric acredula have 8–45 copies15; a bimodal distribution was also confirmed in this new data set (Fig. S2). Accordingly, for the present analyses, we split the data in two groups: birds with ≤6 TE copies and birds with >7, translating into absence or presence of MARB-a, with the former assumed to be homozygous for the absence of MARB-a and the latter heterozygous or homozygous for the presence of MARB-a. Data from two investigated willow warbler families suggest a Mendelian inheritance pattern and provide support for our interpretation of how TE copy numbers reflect the three genotypes (Table S5). Moreover, the TE copy numbers within the hybrid swarm have a distribution similar to a combination of allopatric trochilus and acredula, further supporting that the copies are inherited as intact blocks (haplotypes). However, a precise distinction between heterozygotes and homozygotes on MARB-a is still not possible15.Statistical analysisWe used linear models with departure direction, winter longitude, migration distance and departure timing as response variables and the three genetic markers: MARB-a (a factor with two levels), InvP-Ch1 (a factor with three levels) and InvP-Ch5 (a factor with three levels) as explanatory variables. Models were constructed with R base package “stats”. We reported Type II ANOVA for models with more than one explanatory variable and no interactions and type III ANOVA results for models with interaction term by using R package “Car” (version 3.0-12)28. We initially constructed mixed effect models with timing of departure and tagging year as random factors however, this delivered singular fits due to insufficient sample sizes across categories. Normality of residuals was checked with a Shapiro–Wilk test. For carrying out circular statistics on autumn migration direction we used the R package “circular” (version 0.4-93). Watson’s U2 pairwise comparisons of different groups delivered the same results as linear models (Table S2 and Fig. S5). Circular means were identical to conventional linear means in our data set, which we take as another evidence that linear models are appropriate for the analysis of our data (Table S3 and Fig. S5). Maps in Figs. 1 and 2b and S1, S3 and S4 were created with R package “ggplot2” (version 3.3.6) using continent contours from Natural Earth, naturalearthdata.com/. Heat gradient over the maps in Fig. 1a–d were created with R package “gstat” (version 2.0-8) and the inverse distance weighting power of 3.0. Circular plots were created with ORIANA (version 4.02). All analyses were carried out with R version 4.1.1 (R Core Team 2021).Reporting summaryFurther information on research design is available in the Nature Portfolio Reporting Summary linked to this article. More

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