Table S2.
Population, specimen ID and sample date of modern Atlantic cod specimens
| Population | Specimen_ID | Sample date | Spawning population | No. of reads, millions | Fold coverage |
| Eastern Baltic | ARK_4001 | 2012, May | Yes | 40 | 7.4 |
| Eastern Baltic | ARK_4002 | 2012, May | Yes | 20 | 3.8 |
| Eastern Baltic | ARK_4003 | 2012, May | Yes | 38 | 6.9 |
| Eastern Baltic | ARK_4006 | 2012, May | Yes | 34 | 6.3 |
| Eastern Baltic | ARK_4007 | 2012, May | Yes | 34 | 6.4 |
| Eastern Baltic | ARK_4008 | 2012, May | Yes | 47 | 8.8 |
| Eastern Baltic | ARK_4010 | 2012, May | Yes | 31 | 5.9 |
| Eastern Baltic | ARK_4011 | 2012, May | Yes | 49 | 9.1 |
| Eastern Baltic | ARK_4012 | 2012, May | Yes | 35 | 6.6 |
| Eastern Baltic | ARK_4013 | 2012, May | Yes | 37 | 6.9 |
| Eastern Baltic | ARK_4014 | 2012, May | Yes | 34 | 6.1 |
| Eastern Baltic | ARK_4015 | 2012, May | Yes | 44 | 8.3 |
| Eastern Baltic | ARK_4016 | 2012, May | Yes | 29 | 5.1 |
| Eastern Baltic | ARK_4017 | 2012, May | Yes | 45 | 8.5 |
| Eastern Baltic | ARK_4018 | 2012, May | Yes | 33 | 6.1 |
| Eastern Baltic | ARK_4019 | 2012, May | Yes | 47 | 8.8 |
| Eastern Baltic | ARK_4020 | 2012, May | Yes | 23 | 4.1 |
| Eastern Baltic | ARK_4021 | 2012, May | Yes | 57 | 10.6 |
| Eastern Baltic | ARK_4022 | 2012, May | Yes | 34 | 6.4 |
| Eastern Baltic | ARK_4024 | 2012, May | Yes | 31 | 5.8 |
| Eastern Baltic | ARK_4030 | 2012, May | Yes | 34 | 6.5 |
| Eastern Baltic | ARK_4032 | 2012, May | Yes | 91 | 17.2 |
| Eastern Baltic | ARK_4039 | 2012, May | Yes | 63 | 11.9 |
| Eastern Baltic | ARK_4043 | 2012, May | Yes | 68 | 12.8 |
| Eastern Baltic | BOR_90E | 2011, April | Yes | 44 | 8.3 |
| Eastern Baltic | BOR_91E | 2011, April | Yes | 47 | 9.0 |
| Eastern Baltic | BOR_74E | 2011, May | Yes | 45 | 8.6 |
| Eastern Baltic | BOR_79E | 2011, May | Yes | 50 | 9.6 |
| Eastern Baltic | BOR_60E | 2012, April | Yes | 46 | 8.7 |
| Eastern Baltic | BOR_611E | 2012, May | Yes | 45 | 8.5 |
| Eastern Baltic | BOR_613E | 2012, May | Yes | 43 | 8.2 |
| Eastern Baltic | BOR_614E | 2012, May | Yes | 42 | 7.9 |
| Eastern Baltic | BOR_615E | 2012, May | Yes | 42 | 8.0 |
| Eastern Baltic | BOR_617E | 2012, May | Yes | 41 | 7.8 |
| Eastern Baltic | BOR_621E | 2012, May | Yes | 41 | 7.8 |
| Eastern Baltic | BOR_624E | 2012, May | Yes | 42 | 8.1 |
| Eastern Baltic | BOR_630E | 2012, May | Yes | 40 | 7.5 |
| Eastern Baltic | BOR_655E | 2012, May | Yes | 73 | 13.8 |
| Eastern Baltic | BOR_659E | 2012, May | Yes | 59 | 11.1 |
| Eastern Baltic | BOR_664E | 2012, May | Yes | 66 | 12.5 |
| Eastern Baltic | BOR_AL713 | 2012, May | Yes | 44 | 8.4 |
| Eastern Baltic | BOR_739E | 2012, May | Yes | 57 | 10.8 |
| Eastern Baltic | BOR_749E | 2012, May | Yes | 59 | 11.2 |
| Eastern Baltic | BOR_760E | 2012, May | Yes | 6 | 1.1 |
| Eastern Baltic | BOR_AL724 | 2012, May | Yes | 49 | 9.3 |
| Eastern Baltic | BOR_AL736 | 2012, May | Yes | 44 | 8.4 |
| Eastern Baltic | BOR_AL741 | 2012, May | Yes | 46 | 8.7 |
| Eastern Baltic | BOR_AL777 | 2012, May | Yes | 43 | 8.3 |
| Iceland | I50_02 | 2003, April | Yes | 49 | 10.9 |
| Iceland | I50_03 | 2003, April | Yes | 43 | 9.7 |
| Iceland | I50_04 | 2003, April | Yes | 44 | 9.8 |
| Iceland | I50_05 | 2003, April | Yes | 46 | 10.3 |
| Iceland | I50_06 | 2003, April | Yes | 32 | 7.1 |
| Iceland | I50_07 | 2003, April | Yes | 42 | 9.4 |
| Iceland | I50_08 | 2003, April | Yes | 35 | 7.7 |
| Iceland | I50_09 | 2003, April | Yes | 51 | 11.2 |
| Iceland | I50_10 | 2003, April | Yes | 43 | 9.6 |
| Iceland | I50_11 | 2003, April | Yes | 50 | 11.1 |
| Iceland | I50_12 | 2003, April | Yes | 39 | 8.8 |
| Iceland | I50_13 | 2003, April | Yes | 48 | 10.7 |
| Iceland | I50_14 | 2003, April | Yes | 26 | 5.7 |
| Iceland | I50_15 | 2003, April | Yes | 41 | 9.3 |
| Iceland | I50_16 | 2003, April | Yes | 49 | 11.0 |
| Iceland | I50_17 | 2003, April | Yes | 43 | 9.5 |
| Iceland | I50_18 | 2003, April | Yes | 46 | 10.1 |
| Iceland | I50_19 | 2003, April | Yes | 52 | 11.4 |
| Iceland | I50_20 | 2003, April | Yes | 54 | 12.1 |
| Iceland | I50_23 | 2003, April | Yes | 58 | 12.9 |
| Iceland | I50_26 | 2003, April | Yes | 53 | 10.3 |
| Iceland | I50_38 | 2003, April | Yes | 64 | 12.3 |
| Iceland | I50_41 | 2003, April | Yes | 92 | 19.1 |
| Iceland | I50_42 | 2003, April | Yes | 52 | 11.6 |
| Lofoten | LOF_A_14_01 | 2014, August | No | 60 | 11.4 |
| Lofoten | LOF_A_14_03 | 2014, August | No | 54 | 10.2 |
| Lofoten | LOF_A_14_04 | 2014, August | No | 47 | 9.0 |
| Lofoten | LOF_A_14_05 | 2014, August | No | 47 | 8.9 |
| Lofoten | LOF_A_14_06 | 2014, August | No | 52 | 10.0 |
| Lofoten | LOF_A_14_08 | 2014, August | No | 43 | 8.2 |
| Lofoten | LOF_A_14_09 | 2014, August | No | 50 | 9.5 |
| Lofoten | LOF_A_14_10 | 2014, August | No | 48 | 9.1 |
| Lofoten | LOF_A_14_11 | 2014, August | No | 53 | 10.1 |
| Lofoten | LOF_A_14_16 | 2014, August | No | 54 | 10.1 |
| Lofoten | LOF_A_14_17 | 2014, August | No | 60 | 11.4 |
| Lofoten | LOF_A_14_18 | 2014, August | No | 52 | 9.9 |
| Lofoten | LOF_A_14_19 | 2014, August | No | 54 | 10.3 |
| Lofoten | LOF_A_14_20 | 2014, August | No | 43 | 8.2 |
| Lofoten | LOF_A_14_21 | 2014, August | No | 52 | 9.8 |
| Lofoten | LOF_A_14_22 | 2014, August | No | 48 | 9.1 |
| Lofoten | LOF_A_14_23 | 2014, August | No | 46 | 8.8 |
| Lofoten | LOF_A_14_24 | 2014, August | No | 49 | 9.3 |
| Lofoten | LOF_A_14_25 | 2014, August | No | 59 | 11.2 |
| Lofoten | LOF_A_14_26 | 2014, August | No | 51 | 9.7 |
| Lofoten | LOF_A_14_27 | 2014, August | No | 65 | 12.4 |
| Lofoten | LOF_A_14_28 | 2014, August | No | 49 | 9.3 |
| Lofoten | LOF_A_14_29 | 2014, August | No | 46 | 8.7 |
| Lofoten | LOF_A_14_30 | 2014, August | No | 44 | 8.3 |
| Lofoten | LOF_A_14_33 | 2014, August | No | 46 | 8.8 |
| Lofoten | LOF_A_14_41 | 2014, August | No | 45 | 8.6 |
| Lofoten | LOF_A_14_43 | 2014, August | No | 195 | 37.0 |
| North East Arctic | LOF_M_14_26 | 2014, March | Yes | 46 | 8.7 |
| North East Arctic | LOF_M_14_27 | 2014, March | Yes | 47 | 8.9 |
| North East Arctic | LOF_M_14_28 | 2014, March | Yes | 44 | 8.3 |
| North East Arctic | LOF_M_14_29 | 2014, March | Yes | 46 | 8.6 |
| North East Arctic | LOF_M_14_30 | 2014, March | Yes | 43 | 8.1 |
| North East Arctic | LOF_M_14_31 | 2014, March | Yes | 50 | 9.4 |
| North East Arctic | LOF_M_14_32 | 2014, March | Yes | 50 | 9.4 |
| North East Arctic | LOF_M_14_33 | 2014, March | Yes | 50 | 9.4 |
| North East Arctic | LOF_M_14_35 | 2014, March | Yes | 42 | 8.0 |
| North East Arctic | LOF_M_14_36 | 2014, March | Yes | 53 | 10.0 |
| North East Arctic | LOF_M_14_43 | 2014, March | Yes | 88 | 16.7 |
| North East Arctic | LOF_M_14_44 | 2014, March | Yes | 47 | 9.0 |
| North East Arctic | LOF_M_14_45 | 2014, March | Yes | 45 | 8.6 |
| North East Arctic | LOF_M_14_46 | 2014, March | Yes | 57 | 10.7 |
| North East Arctic | LOF_M_14_47 | 2014, March | Yes | 50 | 9.4 |
| North East Arctic | LOF_M_14_50 | 2014, March | Yes | 39 | 7.4 |
| North East Arctic | LOF_M_14_51 | 2014, March | Yes | 43 | 8.1 |
| North East Arctic | LOF_M_14_52 | 2014, March | Yes | 44 | 8.3 |
| North East Arctic | LOF_M_14_53 | 2014, March | Yes | 24 | 4.5 |
| North East Arctic | LOF_M_14_54 | 2014, March | Yes | 43 | 8.2 |
| North East Arctic | LOF_M_14_55 | 2014, March | Yes | 46 | 8.7 |
| North East Arctic | LOF_M_14_56 | 2014, March | Yes | 55 | 10.5 |
| North East Arctic | LOF_M_14_62 | 2014, March | Yes | 50 | 9.4 |
| North East Arctic | LOF_M_14_68 | 2014, March | Yes | 38 | 7.2 |
| Øresund | ORE_301 | 2012, March | Yes | 44 | 8.2 |
| Øresund | ORE_302 | 2012, March | Yes | 42 | 7.7 |
| Øresund | ORE_303 | 2012, March | Yes | 40 | 7.6 |
| Øresund | ORE_308 | 2012, March | Yes | 33 | 6.0 |
| Øresund | ORE_309 | 2012, March | Yes | 45 | 8.4 |
| Øresund | ORE_310 | 2012, March | Yes | 39 | 7.4 |
| Øresund | ORE_313 | 2012, March | Yes | 105 | 19.8 |
| Øresund | ORE_314 | 2012, March | Yes | 34 | 6.0 |
| Øresund | ORE_315 | 2012, March | Yes | 25 | 4.7 |
| Øresund | ORE_316 | 2012, March | Yes | 49 | 9.3 |
| Øresund | ORE_317 | 2012, March | Yes | 38 | 7.1 |
| Øresund | ORE_318 | 2012, March | Yes | 36 | 6.6 |
| Øresund | ORE_322 | 2012, March | Yes | 33 | 6.0 |
| Øresund | ORE_323 | 2012, March | Yes | 52 | 9.7 |
| Øresund | ORE_325 | 2012, March | Yes | 46 | 8.6 |
| Øresund | ORE_326 | 2012, March | Yes | 39 | 7.2 |
| Øresund | ORE_331 | 2012, March | Yes | 50 | 9.3 |
| Øresund | ORE_332 | 2012, March | Yes | 49 | 9.2 |
| Øresund | ORE_333 | 2012, March | Yes | 48 | 8.9 |
| Øresund | ORE_336 | 2012, March | Yes | 41 | 7.7 |
| Øresund | ORE_341 | 2012, March | Yes | 45 | 8.4 |
| North Sea | SOD_01 | 2002, March | Yes | 43 | 8.3 |
| North Sea | SOD_02 | 2002, March | Yes | 46 | 8.8 |
| North Sea | SOD_03 | 2002, March | Yes | 44 | 8.3 |
| North Sea | SOD_04 | 2002, March | Yes | 55 | 10.4 |
| North Sea | SOD_06 | 2002, March | Yes | 45 | 8.7 |
| North Sea | SOD_07 | 2002, March | Yes | 46 | 8.8 |
| North Sea | SOD_08 | 2002, March | Yes | 42 | 8.1 |
| North Sea | SOD_09 | 2002, March | Yes | 49 | 9.4 |
| North Sea | SOD_10 | 2002, March | Yes | 42 | 8.1 |
| North Sea | SOD_13 | 2002, March | Yes | 43 | 8.3 |
| North Sea | SOD_14 | 2002, March | Yes | 48 | 9.2 |
| North Sea | SOD_15 | 2002, March | Yes | 45 | 8.5 |
| North Sea | SOD_17 | 2002, March | Yes | 46 | 8.7 |
| North Sea | SOD_19 | 2002, March | Yes | 47 | 8.8 |
| North Sea | SOD_20 | 2002, March | Yes | 39 | 7.2 |
| North Sea | SOD_21 | 2002, March | Yes | 45 | 8.3 |
| North Sea | SOD_22 | 2002, March | Yes | 46 | 8.8 |
| North Sea | SOD_23 | 2002, March | Yes | 44 | 8.4 |
| North Sea | SOD_25 | 2002, March | Yes | 45 | 8.6 |
| North Sea | SOD_26 | 2002, March | Yes | 53 | 10.0 |
| North Sea | SOD_27 | 2002, March | Yes | 51 | 9.0 |
| North Sea | SOD_28 | 2002, March | Yes | 46 | 8.6 |
| North Sea | SOD_29 | 2002, March | Yes | 46 | 8.8 |
| North Sea | SOD_30 | 2002, March | Yes | 42 | 7.6 |
We report if sampling took place during spawning, the number of reads obtained, and the resulting fold coverage for the nuclear genome.