Jørn Henrik Sønstebø1†, Adam Vivian-Smith1, Kalev Adamson2, Rein Drenkhan2, Halvor Solheim1 and Ari M

Jørn Henrik Sønstebø1†, Adam Vivian-Smith1, Kalev Adamson2, Rein Drenkhan2, Halvor Solheim1 and Ari M. Hietala1

Genome-wide population diversity in Hymenoscyphus fraxineus points to an eastern Russian origin of European Ash dieback

Supporting Information Contents 1.0 Supplementary Tables

• Supplementary Table 1. Isolate list, GPS locations, ENA accession number and metadata. In a separate Excel table (Supplementary_table1.xlsx). 2.0 Supplementary Figures

• Supplementary. Figure 1. PstI-MspI ddRAD coverage of the H. fraxineus genome (Hfv2). Inaccessible regions of the genome as assessed by to ddRADs. • Supplementary. Figure 2. Boxplot giving the overview of the percentage of the sequenced reads mapping to the genome. • Supplementary. Figure 3. Splitstree Neighbor network including European H fraxineus and H. albidus.

• Supplementary. Figure 4. Genetic differentiation (FST) between H. fraxineus and H. albidus and pairs of populations of H. fraxineus. • Supplementary. Figure 5. The K-mer distribution volume and estimations of the genome size for H. albidus and H. fraxineus. • Supplementary. Figure 6. Principle components analysis at scaffold 1 to 20 of H. fraxineus individuals. • Supplementary. Figure 7. Splitstree Neighbor network including only European H. fraxineus isolates. • Supplementary. Figure 8. Nucleotide diversity π at each scaffold.

• Supplementary. Figure 9. Distribution of fixed and polymorphic blocks.

• Supplementary. Figure 10. Average genetic differentiation (FST) between pair of Russian samples and Norway and Estonia. 3.0 Supplementary Material and Methods

• Method of Whole Genome Amplification (WGA) • Method for calculating genomic fixation 4.0 References

1 Supplementary table 1

Species Sample code Accession number ENA sequence type Country Locality Latitude Longitude Collection date Host species Tissue type Sample type1 DNA isolation2 Collector/sample provider Bayescan group H. fraxineus 4041 ERS1791845 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 26/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4042 ERS1791846 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 19/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4043 ERS1791847 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 11/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4044 ERS1791848 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 30/06/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4045 ERS1791849 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 22/09/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4046 ERS1791850 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 22/09/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4047 ERS1791851 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 15/09/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4048 ERS1791852 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 15/09/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4049 ERS1791853 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 08/09/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4051 ERS1791854 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 01/09/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4052 ERS1791855 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 01/09/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4053 ERS1791856 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 06/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4056 ERS1791857 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 19/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4057 ERS1791858 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 11/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4058 ERS1791859 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 11/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4059 ERS1791860 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 04/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4060 ERS1791861 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 04/08/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4061 ERS1791862 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 28/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4062 ERS1791863 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 28/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4064 ERS1791864 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 28/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4065 ERS1791865 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 21/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4066 ERS1791866 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 21/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4067 ERS1791867 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 14/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4068 ERS1791868 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 14/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4069 ERS1791869 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 07/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4070 ERS1791870 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 07/07/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4071 ERS1791871 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 30/06/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4072 ERS1791872 PstI-MspI ddRAD Estonia Vedu 58.485367 26.756933 30/06/2014 F. excelsior Leaf petiole WAC EZ Kalev Adamson Eur 1 H. fraxineus 4073 ERS1791873 PstI-MspI ddRAD Estonia Valaste 59.444464 27.340558 08/09/2010 F. excelsior Leaf petiole WAC EZ Rein Drenkhan Eur 1 H. fraxineus 4074 ERS1791874 PstI-MspI ddRAD Estonia Sagadi 59.536139 26.084961 09/09/2010 F. excelsior Leaf petiole WAC EZ Rein Drenkhan Eur 1 H. fraxineus 4076 ERS1791875 PstI-MspI ddRAD Estonia Kuusalu 59.46925 25.30205 09/09/2010 F. excelsior Leaf petiole WAC EZ Rein Drenkhan Eur 1 H. fraxineus 4077 ERS1791876 PstI-MspI ddRAD Estonia Oru 59.423175 27.525431 08/09/2010 F. excelsior Leaf petiole WAC EZ Rein Drenkhan Eur 1 H. fraxineus 4080 ERS1791877 PstI-MspI ddRAD Estonia Karula National Park, Viitka 57.732867 26.47795 24/07/2010 F. excelsior Leaf petiole WAC EZ Rein Drenkhan Eur 1 H. fraxineus 2007-107 ERS1791751 PstI-MspI ddRAD Lithuania Birzai, North Eastern Lituania 56.20458 24.70204 N/A F. excelsior shoot necrosis SHI MT Rimvydas Vasaitis H. fraxineus 2007-108 ERS1791752 PstI-MspI ddRAD Lithuania Birzai, North Eastern Lituania 56.20458 24.70204 N/A F. excelsior shoot necrosis VI MT Rimvydas Vasaitis H. fraxineus 2007-109 ERS1791753 PstI-MspI ddRAD Sweden Uppsala, Østerbybruk 60.1894 17.8988 N/A F. excelsior shoot necrosis SHI MT Rimvydas Vasaitis H. fraxineus 2007-110 ERS1791754 PstI-MspI ddRAD Sweden Uppsala, Østerbybruk 60.1894 17.8988 N/A F. excelsior shoot necrosis VI MT Rimvydas Vasaitis H. fraxineus 2008-104/1 ERS1791755 PstI-MspI ddRAD Norway Buskerud, Røyken, Hurum 59.714881 10.4896768 04/06/2008 F. excelsior shoot necrosis SHI MT Ingvald Røsberg Eur2 H. fraxineus 2008-108/2 ERS1791756 PstI-MspI ddRAD Norway Buskerud, Lier, Foss nursery 59.735614 10.4343845 04/06/2008 F. excelsior shoot necrosis SHI MT Ingvald Røsberg Eur2 H. fraxineus 2008-112/2 ERS1791757 PstI-MspI ddRAD Norway Buskerud, Øvre Eiker, RV35, Kverk 59.814093 9.89970998 04/06/2008 F. excelsior shoot necrosis SHI MT Ingvald Røsberg Eur2 H. fraxineus 2008-125/2 ERS1791758 PstI-MspI ddRAD Norway Hedmark, Stange, Espa 60.562573 11.2564499 05/06/2008 F. excelsior shoot necrosis SHI MT Ingvald Røsberg Eur2 H. fraxineus 2008-126/1 ERS1791759 PstI-MspI ddRAD Norway Hedmark, Ringsaker, Tjerne farm 60.834944 10.91020265 06/06/2008 F. excelsior shoot necrosis VI MT Ingvald Røsberg Eur2 H. fraxineus 2008-139/1 ERS1791760 PstI-MspI ddRAD Norway Vest-Agder, Lyngdal, Fleseland 58.099050 7.14595345 08/06/2008 F. excelsior shoot necrosis SHI MT Ingvald Røsberg Eur2 H. fraxineus 2008-142/5 ERS1791761 PstI-MspI ddRAD Norway Vest-Agder, Mandal, RV459, Bringsdal 58.101124 7.53918383 09/06/2008 F. excelsior shoot necrosis VI MT Geir Østreng Eur2 H. fraxineus 2008-143/1 ERS1791762 PstI-MspI ddRAD Norway Vest-Agder, Søgne, Føssa 58.095037 7.79586215 10/06/2008 F. excelsior shoot necrosis SHI MT Geir Østreng Eur2 H. fraxineus 2008-146/5 ERS1791763 PstI-MspI ddRAD Norway Aust-Agder, Lillesand, E18, Vallesved 58.2252485 8.2520134 11/06/2008 F. excelsior shoot necrosis SHI MT Geir Østreng Eur2 H. fraxineus 2008-148/4 ERS1791764 PstI-MspI ddRAD Norway Aust-Agder, Risør, Bossvika 58.718319 9.10315805 12/06/2008 F. excelsior shoot necrosis VI MT Geir Østreng Eur2 H. fraxineus 2008-151/3 ERS1791765 PstI-MspI ddRAD Norway Telemark, Drangedal, RV358, Bostrak 59.101979 8.88752200 09/06/2008 F. excelsior shoot necrosis SHI MT Geir Østreng Eur2 H. fraxineus 2008-152/4 ERS1791766 PstI-MspI ddRAD Norway Telemark, Skien, RV356 Rognsbru 59.113254 9.43448442 10/06/2008 F. excelsior shoot necrosis SHI MT Geir Østreng Eur2 Østfold, Eidsberg, Mysen, Seim nursery, H. fraxineus 2008-165/3 ERS1791767 PstI-MspI ddRAD Norway sent to Sør-Trøndelag, Trondheim, Leira 59.572514 11.2893747 09/07/2008 F. excelsior shoot necrosis VI MT Geir Østreng Eur2 Østfold, Eidsberg, Mysen, Seim nursery, H. fraxineus 2008-166/1 ERS1791768 PstI-MspI ddRAD Norway sent to Sør-Trøndelag, Trondheim, Leira 59.572514 11.2893747 09/07/2008 F. excelsior shoot necrosis SHI MT Halvor Solheim Eur2 H. fraxineus 2008-204/5 ERS1791769 PstI-MspI ddRAD Norway Rogaland: Lund, Moi, along E39. 58.4491981 6.5647775 21/09/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2008-205/1 ERS1791770 PstI-MspI ddRAD Norway Vest-Agder, Kvinesdal, Likenes 58.321701 6.97635998 21/09/2008 F. excelsior shoot necrosis SHI MT Geir Østreng Eur2 H. fraxineus 2008-29/1 ERS1791771 PstI-MspI ddRAD Norway Østfold, Rygge, nursery, (Norsk 59.386705 10.6814292 26/05/2008 F. excelsior shoot necrosis SHI MT Geir Østreng Eur2 H. fraxineus 2008-30/3 ERS1791772 PstI-MspI ddRAD Norway Østfold, Rygge, nursery, (Norsk 59.386705 10.6814292 26/05/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2008-32/4 ERS1791773 PstI-MspI ddRAD Norway Østfold, Rygge, ved skytebane 59.371261 10.7243110 26/05/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2008-77/4 ERS1791774 PstI-MspI ddRAD Norway Østfold, Eidsberg, Mysen, Seim nursery 59.572514 11.2893747 27/05/2008 F. excelsior shoot necrosis SHI MT Halvor Solheim Eur2 H. fraxineus 2008-78/3 ERS1791775 PstI-MspI ddRAD Norway Østfold, Eidsberg, Mysen, Seim nursery 59.572514 11.2893747 27/05/2008 F. excelsior shoot necrosis SHI MT Halvor Solheim Eur2 H. fraxineus 2008-79/1 ERS1791776 PstI-MspI ddRAD Norway Østfold, Eidsberg, Mysen, Seim nursery 59.572514 11.2893747 27/05/2008 F. excelsior shoot necrosis SHI MT Halvor Solheim Eur2 H. fraxineus 2008-80/3 ERS1791777 PstI-MspI ddRAD Norway Østfold, Askim, Rustad nursery 59.59441 11.10273 27/05/2008 F. excelsior shoot necrosis SHI MT Halvor Solheim Eur2 H. fraxineus 2008-81/6 ERS1791778 PstI-MspI ddRAD Norway Østfold, Askim, Rustad nursery 59.59441 11.10273 27/05/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2008-82/2 ERS1791779 PstI-MspI ddRAD Norway Østfold, Askim, Rustad nursery 59.59441 11.10273 27/05/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2008-84/1 ERS1791781 PstI-MspI ddRAD Norway Østfold, Askim, Rustad nursery 59.59441 11.10273 27/05/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2008-85/3 ERS1791782 PstI-MspI ddRAD Norway Østfold, Askim, Rustad nursery 59.59441 11.10273 27/05/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2008-88/3 ERS1791783 PstI-MspI ddRAD Norway Akershus, Ullensaker, Jessheim 60.13466 11.17647 29/05/2008 F. excelsior shoot necrosis VI MT Halvor Solheim Eur2 H. fraxineus 2009-106/2/1 ERS1791786 PstI-MspI ddRAD Norway Akershus, Ås, Norderås, Askehagan 59.6814721 10.7764235 04/06/2008 F. excelsior mycelia SSI MT Halvor Solheim Eur2 H. fraxineus 2009-107/3/1 ERS1791787 PstI-MspI ddRAD Norway Akershus, Vestby, Son, Kolås skog 59.5364935 10.711417 29/07/2008 F. excelsior mycelia SSI MT V. Timmermann & I Børja Eur2 H. fraxineus 2009-109/4/1 ERS1791788 PstI-MspI ddRAD Norway Vestfold, Sandefjord, Fevang 59.198004 10.2354864 11/08/2008 F. excelsior mycelia SSI MT Volkmar Timmermann Eur2

2 H. fraxineus 2009-112/1/1 ERS1791789 PstI-MspI ddRAD Norway Vestfold, Horten, Fjugstad 59.361899 10.457551 18/08/2008 F. excelsior mycelia SSI MT Volkmar Timmermann Eur2 H. fraxineus 2009-112/1/3 ERS1791790 PstI-MspI ddRAD Norway Vestfold, Horten, Fjugstad 59.361899 10.457551 18/08/2008 F. excelsior mycelia PSI MT Volkmar Timmermann Eur2 H. fraxineus 2009-112/2/2 ERS1791784 PstI-MspI ddRAD Norway Vestfold, Horten, Fjugstad 59.361899 10.457551 18/08/2008 F. excelsior mycelia SSI MT Volkmar Timmermann Eur2 H. fraxineus 2009-112/3/1 ERS1791791 PstI-MspI ddRAD Norway Vestfold, Horten, Fjugstad 59.361899 10.457551 18/08/2008 F. excelsior mycelia SSI MT Volkmar Timmermann Eur2 H. fraxineus 2009-86/3 ERS1791785 PstI-MspI ddRAD Norway Rogaland, Eigersund, Litle Hogstad 58.53963 6.16204 25/05/2009 F. excelsior shoot necrosis VI MT Volkmar Timmermann Eur2 H. fraxineus 2010-185/2 ERS1791792 PstI-MspI ddRAD Norway Rogaland, Suldal, Ropeid/Sand 59.4902097 6.2019041 04/09/2010 F. excelsior shoot necrosis VI MT Halvor Solheim H. fraxineus 2010-189/4 ERS1791793 PstI-MspI ddRAD Norway Rogaland, Bjerkheim, Vikeså 58.637790 6.0861592 01/09/2010 F. excelsior shoot necrosis VI MT Ingvald Røsberg H. fraxineus 2010-189/5 ERS1791794 PstI-MspI ddRAD Norway Rogaland, Bjerkheim, Vikeså 58.637790 6.0861592 01/09/2010 F. excelsior shoot necrosis VI MT Halvor Solheim H. fraxineus 2011-10/5/1 ERS1791795 PstI-MspI ddRAD Norway Hordaland, Kvinnherad, Handaland, 59.818142 5.8063125 26/05/2011 F. excelsior shoot necrosis SHI MT Halvor Solheim H. fraxineus 2011-12/1 ERS1791797 PstI-MspI ddRAD Norway Rogaland, Vindafjord, Longaland 59.480843 6.0529906 26/05/2011 F. excelsior shoot necrosis SHI MT Halvor Solheim H. fraxineus 2011-9/1 ERS1791799 PstI-MspI ddRAD Norway Hordaland, Fitjar, Eide 59.922185 5.4762242 27/05/2011 F. excelsior shoot necrosis VI MT Halvor Solheim H. fraxineus 2011-10/5/3 ERS1791796 PstI-MspI ddRAD Norway Hordaland, Kvinnherad, Uskedal 59.928071 5.8486652 26/05/2011 F. excelsior shoot necrosis VI MT Halvor Solheim H. fraxineus 2011-8/1/2 ERS1791798 PstI-MspI ddRAD Norway Rogaland, Sauda, Sauda, Treåskjeret 59.644737 6.3357045 26/05/2011 F. excelsior shoot necrosis SHI MT Halvor Solheim H. fraxineus 2012-24/1 ERS1791800 PstI-MspI ddRAD Norway Sogn og Fjordane, Askvold, Rivedal 61.361516 5.2560764 22/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-25/2 ERS1791801 PstI-MspI ddRAD Norway Sogn og Fjordane, Flora, Droga 61.501144 5.2555345 25/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-29/2/2 ERS1791802 PstI-MspI ddRAD Norway Sogn og Fjordane, Leikanger, Klyvi 61.173067 6.87168032 22/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-32/1/1 ERS1791803 PstI-MspI ddRAD Norway Sogn og Fjordane, Aurland, 60.905233 7.1959603 26/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-38/2/2 ERS1791804 PstI-MspI ddRAD Norway Sogn og Fjordane, Stryn, Innvik 61.8441226 6.6042887 23/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-39/1/2 ERS1791805 PstI-MspI ddRAD Norway Sogn og Fjordane, Stryn, Innvik 61.842422 6.5998417 23/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-42/1/1 ERS1791806 PstI-MspI ddRAD Norway Sogn og Fjordane, Flora, Droga 61.501144 5.2555345 23/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-44/1/2 ERS1791807 PstI-MspI ddRAD Norway Sogn og Fjordane, Luster, Luster sentrum 61.446038 7.4628573 25/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2012-46/4 ERS1791808 PstI-MspI ddRAD Norway Sogn og Fjordane, Naustdal, Bergplassen 61.504046 5.7562401 23/06/2012 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-49 ERS1791809 PstI-MspI ddRAD Norway Møre og Romsdal, Vanylven, Hjellegjerde 62.402887 6.5738008 12/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-51 ERS1791810 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.481008 6.7827516 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-53 ERS1791811 PstI-MspI ddRAD Norway Møre og Romsdal, Ørstad Sæbø 62.213547 6.4784224 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-54 ERS1791812 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.480796 6.7925679 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-55 ERS1791813 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.481032 6.7915608 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-56 ERS1791814 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.481403 6.7787633 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-57 ERS1791815 PstI-MspI ddRAD Norway Møre og Romsdal, Stranda, Hellesylt 62.087298 6.8676982 12/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-58 ERS1791816 PstI-MspI ddRAD Norway Møre og Romsdal, Ørstad, Sandvika 62.231899 6.0093697 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-59 ERS1791817 PstI-MspI ddRAD Norway Møre og Romsdal, Stordal, Dyrkorn 62.421490 6.9459563 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-61 ERS1791818 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.481067 6.7745769 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-63 ERS1791819 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.477854 6.7629208 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-65 ERS1791820 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.477641 6.7569599 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-68 ERS1791821 PstI-MspI ddRAD Norway Møre og Romsdal, Rauma, Måndalen 62.53798735 7.4362958 09/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-69 ERS1791822 PstI-MspI ddRAD Norway Møre og Romsdal, Skodje, Honningdal 62.46405861 6.6113966 09/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-70-2 ERS1791823 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.48108159 6.7977296 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-71 ERS1791824 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.47753851 6.7579391 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-72 ERS1791825 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.4812037 6.7997778 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-73 ERS1791826 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.48096356 6.7970785 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-74 ERS1791827 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.47773798 6.7608543 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-76 ERS1791828 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.4778473 6.7626314 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-77 ERS1791829 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.48141857 6.7787633 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-79 ERS1791830 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.4774632 6.75940017 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-84 ERS1791831 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.4808993 6.7901744 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-85 ERS1791832 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.4811032 6.7747500 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-86 ERS1791833 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.48034609 6.7734479 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-87 ERS1791834 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.48129339 6.7997712 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-88 ERS1791835 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.48141857 6.7787633 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-90 ERS1791836 PstI-MspI ddRAD Norway Møre og Romsdal, Rauma, Grytten 62.55258389 7.6714257 09/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 2014-93 ERS1791837 PstI-MspI ddRAD Norway Møre og Romsdal, Ørskog, Sjøholt 62.47785782 6.7627276 10/08/2014 F. excelsior shoot necrosis VI MT Halvor Solheim Eur3 H. fraxineus 951_FB ERS1791929 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior ascocarp WAC MT Ari Hietala H. fraxineus 2015_951_5 ERS1791842 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior mycelia SSI MT Ari Hietala H. fraxineus 2015_951_7 ERS1791843 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior mycelia SSI WGA Ari Hietala H. fraxineus 2015_951_8 ERS1791844 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior mycelia SSI MT Ari Hietala H. fraxineus 2015_951_11 ERS1791838 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior mycelia SSI WGA Ari Hietala H. fraxineus 2015_951_12 ERS1791839 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior mycelia SSI MT Ari Hietala H. fraxineus 2015_951_22 ERS1791840 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior mycelia SSI WGA Ari Hietala H. fraxineus 2015_951_23 ERS1791841 PstI-MspI ddRAD Norway Akershus, Ås, Norderås 59.4044 10.46031 11/08/2015 F. excelsior mycelia SSI MT Ari Hietala H. fraxineus 4083 ERS1791878 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Gostinitsa 43.05066 131.862 26/08/2014 F. rhynchophylla leaf petiole WAC EZ Halvor Solheim Rus1 H. fraxineus 4084 ERS1791879 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Gostinitsa 43.05066 131.862 26/08/2014 F. rhynchophylla leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4085 ERS1791880 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Gostinitsa 43.05066 131.862 26/08/2014 F. rhynchophylla leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4086 ERS1791881 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Gostinitsa 43.05066 131.862 26/08/2014 F. rhynchophylla leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4087 ERS1791882 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Ostrov 43.01985 131.86503 26/08/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4088 ERS1791883 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Ostrov 43.01985 131.86503 26/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4089 ERS1791884 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Ostrov 43.01985 131.86503 26/08/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4090 ERS1791885 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Ostrov 43.01985 131.86503 26/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4091 ERS1791886 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Ostrov 43.01985 131.86503 26/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4092 ERS1791887 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Ostrov 43.01985 131.86503 26/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4094 ERS1791888 PstI-MspI ddRAD Far East Russia Primorskij, Vladivostok, Botanical garden 43.22405 131.99187 29/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4095 ERS1791889 PstI-MspI ddRAD Far East Russia Primorskij, Vladivostok, Botanical garden 43.22405 131.99187 29/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4096 ERS1791890 PstI-MspI ddRAD Far East Russia Primorskij, Vladivostok, Botanical garden 43.22405 131.99187 29/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1

3 H. fraxineus 4099 ERS1791891 PstI-MspI ddRAD Far East Russia Primorskij, Nikolaevka 43.86233 132.4669 27/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 4102 ERS1791892 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4103 ERS1791893 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4104 ERS1791894 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4108 ERS1791895 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4109 ERS1791896 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. rhynchophylla leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4110 ERS1791897 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4112 ERS1791898 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4114 ERS1791899 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4115 ERS1791900 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4116 ERS1791901 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 4117 ERS1791902 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28299 134.83318 01/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4119 ERS1791903 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28299 134.83318 01/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4120 ERS1791904 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28299 134.83318 01/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4121 ERS1791905 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28299 134.83318 01/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4122 ERS1791906 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28791 134.80344 01/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4123 ERS1791907 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28791 134.80344 01/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4124 ERS1791908 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28791 134.80344 01/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4125 ERS1791909 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28791 134.80344 01/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4126 ERS1791910 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.28791 134.80344 01/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4132 ERS1791911 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.27472 134.88333 02/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4133 ERS1791912 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.27472 134.88333 02/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4134 ERS1791913 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.27472 134.88333 02/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4135 ERS1791914 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.27472 134.88333 02/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4138 ERS1791915 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.26629 134.89319 02/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4140 ERS1791916 PstI-MspI ddRAD Far East Russia Khabarovskij, Bychikha 48.30509 134.81162 04/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4141 ERS1791917 PstI-MspI ddRAD Far East Russia Khabarovskij, Bychikha 48.30509 134.81162 04/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4142 ERS1791918 PstI-MspI ddRAD Far East Russia Khabarovskij, Bychikha 48.30509 134.81162 04/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim H. fraxineus 4143 ERS1791919 PstI-MspI ddRAD Far East Russia Khabarovskij, Bychikha 48.30509 134.81162 04/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4144 ERS1791920 PstI-MspI ddRAD Far East Russia Khabarovskij, Bychikha 48.30509 134.81162 04/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 4145 ERS1791921 PstI-MspI ddRAD Far East Russia Khabarovskij, Bychikha 48.30509 134.81162 04/09/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 416-R2 ERS1791922 PstI-MspI ddRAD Far East Russia Primorskij, Russky island, Gostinitsa 43.05066 131.862 26/08/2014 Fraxinus sp. leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus1 H. fraxineus 421-2 ERS1791923 PstI-MspI ddRAD Far East Russia Primorskij, Nikolaevka 43.86233 132.4669 27/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 421-4 ERS1791924 PstI-MspI ddRAD Far East Russia Primorskij, Nikolaevka 43.86233 132.4669 27/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 425-24 ERS1791925 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 425-26 ERS1791926 PstI-MspI ddRAD Far East Russia Primorskij, Ussuri nature reserve 43.64415 132.34388 28/08/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus2 H. fraxineus 439-19 ERS1791927 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.27472 134.88333 02/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3 H. fraxineus 439-6 ERS1791928 PstI-MspI ddRAD Far East Russia Khabarovskij, Bolshekhekhtsirsky Nature 48.27472 134.88333 02/09/2014 F. mandshurica leaf petiole WAC EZ R. Drenkhan & H. Solheim Rus3

H. fraxineus FC-1445 TNS-F-12761 ERS1791939 PstI-MspI ddRAD Japan Nagano, Sugadaira, 36.5251 138.3476 N/A F. mandshurica leaf petiole SSI WGA Zhao et al., 2013 H. fraxineus FC-2793 TNS-F-40043 ERS1791940 PstI-MspI ddRAD Japan Hokkaido, Yubari 43.0502 141.9692 N/A F. mandshurica leaf petiole SSI WGA Zhao et al., 2013 H. fraxineus FC-2799 TNS-F-40051 ERS1791941 PstI-MspI ddRAD Japan Hokkaido, Chitose 42.8172 141.6419 N/A F. mandshurica leaf petiole SSI MT Zhao et al., 2013 H. fraxineus FC-5343 TNS-F-51807 ERS1791943 PstI-MspI ddRAD Japan Nagano, Kayanodaira, Kijimadaira-mura, 36.7501 138.0667 07/08/2013 F. mandshurica leaf petiole SSI MT Zhao et al., 2013 H. fraxineus FC-5085 TNS-F-40150 ERS1791942 PstI-MspI ddRAD Japan Nagano, Sugadaira, 36.5251 138.3476 15/09/2012 F. mandshurica leaf petiole SSI WGA Zhao et al., 2013

H. fraxineus CBS 122191 ERS1791930 PstI-MspI ddRAD Austria Upper Austria, Edt bei Lambach 48.109192 13.875133 20/06/2007 F. excelsior N/A N/A MT E Halmsclager & S Mottinger-Kroupa H. fraxineus CBS 122192 ERS1791931 PstI-MspI ddRAD Austria Styria 47.359313 14.470012 20/06/2006 F. excelsior N/A N/A MT E Halmsclager & S Mottinger-Kroupa H. fraxineus CBS 122193 ERS1791932 PstI-MspI ddRAD Austria Upper Austria, Bio-Hof Brückler, Laussa 47.940934 14.487323 25/07/2007 F. excelsior N/A N/A MT E Halmsclager & S Mottinger-Kroupa H. fraxineus CBS 122503 ERS1791933 PstI-MspI ddRAD Poland Andrychow 49.854894 19.341281 11/07/2005 F. excelsior N/A N/A MT T. Kowalski H. fraxineus CBS 122504 ERS1791934 PstI-MspI ddRAD Poland Wloszczowa 50.85246 19.967691 06/12/2000 F. excelsior shoot necrosis VI MT T. Kowalski H. fraxineus CBS 122505 ERS1791935 PstI-MspI ddRAD Poland Limanowa 49.705912 20.422575 21/06/2005 F. excelsior dead shoot VI MT T. Kowalski H. fraxineus CBS 122506 ERS1791936 PstI-MspI ddRAD Poland Miechow 50.356893 20.027431 12/06/2004 F. excelsior shoot necrosis VI MT T. Kowalski H. fraxineus CBS 122507 ERS1791937 PstI-MspI ddRAD Poland Wtoszczova 50.85246 19.967691 06/12/2000 F. excelsior shoot necrosis VI MT T. Kowalski H. fraxineus CBS 122509 ERS1791938 PstI-MspI ddRAD Poland Niepotomice 50.025646 20.231949 20/05/2005 F. excelsior dead shoot VI MT T. Kowalski H. albidus CBS 126533 ERS1791953 PstI-MspI ddRAD Switzerland Valais, Leukerbad (Loèche-Les Bains) 46.381002 7.626453 09/08/2012 F. excelsior leaf petiole VI MT O. Holdenrieder H. albidus 2009-124/3/1 ERS1791952 PstI-MspI ddRAD Norway Hordaland, Bergen, Arboretum at Milde 60.2517666 5.2699337 17/08/2009 F. excelsior mycelia SSI MT Terhi Pousi H. albidus 2009-124/1/1 ERS1791951 PstI-MspI ddRAD Norway Hordaland, Bergen, Arboretum at Milde 60.2517666 5.2699337 17/08/2009 F. excelsior mycelia SSI MT Terhi Pousi H. albidus 2009-111/1/1 ERS1791950 PstI-MspI ddRAD Norway Hordaland, Bergen, Arboretum at Milde 60.2517666 5.2699337 14/08/2009 F. excelsior mycelia SSI MT Terhi Pousi H. albidus 2009-111/1/4 ERS1791949 PstI-MspI ddRAD Norway Hordaland, Bergen, Arboretum at Milde 60.2517666 5.2699337 14/08/2009 F. excelsior mycelia PSI MT Terhi Pousi

H. fraxineus 2009-112/1/3 PRJEB21336 WGS Norway Vestfold, Horten, Fjugstad 59.361899 10.457551 18/08/2008 F. excelsior mycelia PSI MT Volkmar Timmermann H. albidus 2009-111/1/4 PRJEB21336 WGS Norway Hordaland, Bergen, Arboretum at Milde 60.2517666 5.2699337 14/08/2009 F. excelsior mycelia PSI MT Terhi Pousi

1 Tissue type: WAC = whole ascocarp, VI = vegetative isolate - single hyphae, SSI = single ascospore isolate, PSI = polyspore isolate, SHI= single hypha isolate 2 DNA extraction or amplification method: EZ = E.Z.N.A Fungal DNA Kit, MT = Invitrogen Mouse Tail #8, WGA = Repli-G Whole Genome Amplification from mycelia

Supplementary. Figure 1. PstI-MspI ddRAD coverage of the H. fraxineus genome (Hfv2). Inaccessible regions of the genome as assessed by to ddRADs. Areas of the genome which were not assessed by ddRAD analysis due to poor coverage or enzyme site bias.

5 Supplementary. Figure 2. Boxplot giving the overview of the percentage of the sequenced reads mapping to the genome. CBS (cultures from different parts of Europe), Japan and Norway represent cultures isolated from single spores and single hyphae of Hymenoscyphus fraxineus. H.albidus also comes from cultures, while the samples from Russia and Estonia are from fruitbodies.

Supplementary. Figure 3. Splitstree Neighbor network including European H fraxineus and H. albidus. All samples of H. albidus were unique compared to H fraxineus.

A 6 H. fraxineus

5 H. albidus

% volume kmer% 2

0 10 20 30 40 50 60 25mer coverage depth B

Species isolate kmer count peak genome GC used reads used bases read depth size (Mb) % length (million) (billion) (bp)

H. fraxineus 112_1_3 53627242 18 63.0 42.5 7.72 1.768 200-250

H. albidus 111_1_4 45935113 18 53.0 44.9 7.14 1.423 200-250

Supplementary. Figure 4A. The K-mer distribution volume using K-mer counting Jellyfish v2.0 (Marçais and Kingsford, 2011), and Figure 4B, the estimation of Hymenoscyphus genome size based on the K-mer distribution. Percentage K-mer volume was plotted against 25 K-mer depth for H. fraxineus and H. albidus. Low frequency K-mers contain essentially random sequencing errors and have low coverage depth (<5), while more repetitive sequences are found at higher 25mer coverage depths.

Supplementary. Figure 5. Genetic differentiation (FST) between H. fraxineus and H. albidus and pairs of populations of H. fraxineus.

Supplementary. Figure 6. Principle components analysis at scaffold 1 to 20 of H. fraxineus individuals

10 Supplementary. Figure 7. Splitstree Neighbor network including only European H. fraxineus isolates, where the samples are color coded based on their origin (red for Norway, blue for Estonia and green for other European origin).

Supplementary. Figure 8. Nucleotide diversity π at each scaffold. Nucleotide divergence was calculated in windows of 20 kb in European (black) and Asian (red) individuals. The horizontal lines show the average diversity in Europe (black) and Asia (red).

Supplementary. Figure 9. Distribution of tracts for genomic fixation and the segmented diversity islands. Historically fixed tracts with very low genetic diversity (top) and segments of the polymorphic diversity islands (bottom).

Supplementary. Figure 10. Average genetic differentiation (FST) between pair of Russian samples and Norway and Estonia. The analysis shows a similarly low genetic differentiation among pairs of samples.

14 Supplementary Material and Methods Method of Whole Genome Amplification (WGA) DNA was also prepared from mycelia and other tissues, and low quantity DNA samples, using isothermal amplification. In the cases of tissue samples, a small sample of approximately 0.5 mm in diameter was scrapped from mycelium using a sterile pipette tip or a scalpel blade and this was suspended in 5 µl of sterile nuclease free water in a DNA Low Bind Eppendorf tube (Eppendorf, Hamburg, Germany) and vortexed. The Eppendorf was then freeze-thawed by five cyclic transfers between liquid nitrogen and a water bath at room temperature. DNA was amplified by the REPLI-g Single Cell Kit WGA (Catalogue ID #150343; Qiagen, www.qiagen.com), as per protocol using 1µl as input into the standard reaction volume. Reactions were amplified at for 8 h with a Veriti thermal cycler (ThermoFisher). WGA reactions were cleaned further with Ampure XP into 25 µl and the DNA quantified with a Qubit Broad Range DNA assay (ThermoFisher). Preparations from WGA provided an advantage and shortened mycelial culture times.

Method for calculating genomic fixation

The length of the fixed and polymorphic segments was calculated using the p values calculated for 20kbp windows and 5 Kbp step. Every window with a p value above 0.00001 was determined as polymorphic, while windows below were determined as fixed. The number of consecutive windows was recorded in R and the average length of the polymorphic and fixed sections were calculated. The limit of 0.00001 was used since we expect that regions with lower value are primarily the result of recent mutations or sequencing errors.

References:

Marçais, G., and Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-70