Supporting information Accumulation and purging of deleterious mutations through severe bottlenecks in ibex Christine Grossen1,*, Frederic Guillaume1, Lukas F. Keller1,a,*, Daniel Croll2,a,* 1Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland 2Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland a, LFK and DC contributed equally to this work *Authors for correspondence: [email protected], [email protected], [email protected] TABLE OF CONTENTS Figure S1 .............................................................................................................................................................................. 3 Figure S2A ........................................................................................................................................................................... 3 Figure S2B ........................................................................................................................................................................... 3 Figure S3A ........................................................................................................................................................................... 4 Figure S3B ........................................................................................................................................................................... 5 Figures S4A - S4D ............................................................................................................................................................... 6 Figures S5A - S5D ............................................................................................................................................................... 7 Figure S5A ........................................................................................................................................................................... 7 Figure S6 .............................................................................................................................................................................. 8 Figure S7A ........................................................................................................................................................................... 8 Figure S7B ........................................................................................................................................................................... 9 Figure S7C ........................................................................................................................................................................... 9 Figure S7D ......................................................................................................................................................................... 10 Figure S8 ............................................................................................................................................................................ 11 Figure S9A ......................................................................................................................................................................... 12 Figure S9B ......................................................................................................................................................................... 12 Figure S10 .......................................................................................................................................................................... 13 Figure S11A ....................................................................................................................................................................... 14 Figure S11B ....................................................................................................................................................................... 14 Figure S12 .......................................................................................................................................................................... 15 Figure S13 .......................................................................................................................................................................... 16 Figure S14 .......................................................................................................................................................................... 16 Figure S16 .......................................................................................................................................................................... 18 Figure S17 .......................................................................................................................................................................... 19 Figure S18 .......................................................................................................................................................................... 20 Figure S19 .......................................................................................................................................................................... 21 Figure S20 .......................................................................................................................................................................... 22 Figures S21 - S28 ............................................................................................................................................................... 23 Figures S30 - S37 ............................................................................................................................................................... 28 Table S1A .......................................................................................................................................................................... 33 Table S1B ........................................................................................................................................................................... 34 Table S2 ............................................................................................................................................................................. 35 Table S3 ............................................................................................................................................................................. 36 Table S4 ............................................................................................................................................................................. 38 Table S5 ............................................................................................................................................................................. 38 Table S6 ............................................................................................................................................................................. 39 Supplementary File S1 ....................................................................................................................................................... 40 Grossen et al. 2 Supplementary Information SUPPLEMENTARY FIGURES Figure S1: Principal component analysis including all ibex species under study. Colors indicate different species. 2.0 1.5 1.0 0.5 ● Heterozygous SNPs per KB 0.0 ib py fa nu si ae hi Species Figure S2A: Genome-wide heterozygosity per species represented as number of heterozygous autosomal SNPs per kb. ib: Capra ibex, py: C. pyrenaica, fa: C. falconeri, nu: C. nubiana, si: C. sibirica, ae: C. aegagrus, hi: C. hircus. 4e−04 2e−04 Heterozygous SNPs per KB 0e+00 ib py fal nu si ae hi Species Figure S2B: Genome-wide heterozygosity per species in coding sequences (CDS) represented as number of heterozygous SNPs per kb of CDS. ib: Capra ibex, py: C. pyrenaica, fa: C. falconeri, nu: C. nubiana, si: C. sibirica, ae: C. aegagrus, hi: C. hircus. Grossen et al. 3 Supplementary Information 1 ib.08S.12F_am ib.06S.12M_am ib.22S.12F_am ib.VS0102_mi ib.VS0079_wh ib.VS0081_wh ib.VS0031_wh ib.BE0309_bo ib.BE0407_bo ib.BE0463_bo ib.GR0140_rh ib.NW0045_ob ib.NW0061_ob ib.UR0036_ob ib.VS0139_pl ib.VS1121_pl ib.VS1124_pl ib.BE0010_br ib.BE0283_br ib.OW0002_br ib.GR0201_al ib.GR0323_al ib.GR0442_al ib.GPR21C_gp ib.GPV05C_gp ib.GPV18C_gp ib.GPO03D_gp ib.GPO39B_gp species ib.GPV09K_gp Cahi ib.GPV13G_gp Caae Cafal py.M518_sn Canu py.Z5_hb Casi py.V53_vi Capy Caib py.V66_vi si.Casi1 si.Casi2 nu.ibx20 nu.ibx61 fal.Cafal1 IRCA−C3−1001 IRCA−G2−5063 IRCA−I11−0001 IRCA−I6−5237 IRCA−K12−0005 IRCA−M12−0008 hi.PCGA06 AUST_Boer_942a AUST_Cash_E040 AUST_RL_100a FRCH−AL−0002 FRCH−SA−0001 IRCH−F3−5044 IRCH−F4−5093 IRCH−G5−5185 ITCH−SA−0001 ITCH−SA−0005 MOCH−L10−3100 MOCH−Q15−1143 MOCH−R5−0037 MOCH−S8−2252 MOCH−V5−3059 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 Chromosomal position [Mb] Figure S3A: Runs of homozygosity (ROH) along chromosome 1. Bcftools analysis with viterbi- training option turned off. The alternative allele frequency prior was set to 0.4. Colors represent species as in Figures S1 and S2. Caib: Capra ibex, Capy: C. pyrenaica, Cafal: C. falconeri, Canu: C. nubiana, Casi: C. sibirica, Caae: C. aegagrus, Cahi: C. hircus. Grossen et al. 4 Supplementary Information 1 ib.08S.12F_am ib.06S.12M_am ib.22S.12F_am ib.VS0102_mi