I re-simulated the data with SLiM 4.0.0, however, I found the neutral SFS are different from the previous simulated data from SLiM 3.7.1 if using annotation. For example, for genetic_map=HapMapII_GRCh37, demography=Constant, dfe=Gamma_H17, annotation=ensembl_havana_104_exons, seed=1069045866, chr=chr21, pop=pop0,
If not using annotation, then both neutral and non-neutral SFS are similar.
For genetic_map=HapMapII_GRCh37, demography=Constant, dfe=Gamma_H17, annotation=all_sites, seed=1069045866, chr=chr21, pop=pop0
I re-simulated the data with SLiM 4.0.0, however, I found the neutral SFS are different from the previous simulated data from SLiM 3.7.1 if using annotation. For example, for
genetic_map=HapMapII_GRCh37, demography=Constant, dfe=Gamma_H17, annotation=ensembl_havana_104_exons, seed=1069045866, chr=chr21, pop=pop0,the neutral SFS from SLiM 4.0.0 is
[0 18237 8492 5629 4418 3439 2799 2928 2033 1784 1712 1706 1369 1353 1218 1281 1095 930 863 1004 934 827 760 680 703 744 818 541 768 558 634 522 674 487 436 903 353 495 459 881 457 379 416 378 352 312 475 344 362 350 330 298 316 322 376 227 243 285 264 269 308 619 276 290 183 249 222 246 256 215 325 190 217 173 197 249 173 180 235 294 261 255 207 231 250 227 239 179 136 174 195 116 137 150 112 157 162 160 188 208 0]while the neutral SFS from SLiM 3.7.1 is
[0 103 50 37 25 14 12 18 9 12 6 6 4 7 5 5 9 1 4 5 4 7 4 4 0 10 3 8 3 1 3 3 1 1 3 3 2 4 2 0 1 7 2 2 7 1 4 3 2 1 1 2 2 1 0 3 3 3 1 2 0 3 5 3 2 1 0 4 0 0 0 1 1 5 1 0 0 1 1 0 0 1 0 2 4 0 0 1 2 2 3 0 0 3 0 1 3 1 0 5 0]However, the non-neutral SFS are similar. The non-neutral SFS from SLiM 4.0.0 is
[0 183 62 39 27 23 19 21 12 10 10 6 7 5 6 10 5 2 11 3 5 6 5 4 3 8 1 2 2 0 3 2 7 2 1 2 2 4 3 1 1 1 3 0 1 1 1 0 1 3 2 1 0 2 4 0 4 1 2 2 0 1 2 0 2 3 0 1 2 1 0 1 2 0 0 0 0 0 3 0 0 1 0 0 0 1 1 0 0 1 2 0 0 0 0 0 1 0 0 1 119]And the one from SLiM 3.7.1 is
[0 151 45 29 24 21 17 21 19 6 10 7 4 5 2 1 9 4 3 3 7 1 2 5 3 3 3 3 5 2 2 0 2 2 2 2 3 3 1 2 0 2 3 1 0 1 1 1 0 0 0 1 1 0 4 2 4 0 4 1 0 1 0 1 1 3 1 1 2 0 2 0 2 0 1 1 0 1 0 1 1 0 0 0 2 1 0 0 0 1 3 0 1 2 0 0 1 0 0 0 127]If not using annotation, then both neutral and non-neutral SFS are similar. For
genetic_map=HapMapII_GRCh37, demography=Constant, dfe=Gamma_H17, annotation=all_sites, seed=1069045866, chr=chr21, pop=pop0The neutral SFS from SLiM 4.0.0 is
[0 3682 1604 1057 711 517 440 324 282 216 233 231 200 204 173 149 139 130 156 126 110 93 90 94 104 78 94 64 60 67 62 75 55 52 48 54 53 49 56 61 51 41 43 42 36 45 47 46 35 33 49 31 36 36 36 29 26 44 18 37 41 34 19 35 24 24 23 30 35 30 16 22 26 20 24 21 25 32 35 30 22 32 25 36 26 24 30 26 26 20 34 27 18 22 15 26 43 44 19 32 0]The neutral SFS from SLiM 3.7.1 is
[0 3928 1649 1006 798 603 462 389 335 284 259 242 179 189 170 143 139 156 181 89 111 111 105 99 90 80 93 86 71 83 59 75 74 75 64 71 51 39 74 41 61 59 59 41 47 42 58 46 39 63 55 38 46 42 27 35 47 30 27 37 42 23 34 30 22 28 32 37 35 32 24 27 42 46 58 22 29 34 39 37 30 22 39 38 31 42 36 19 32 34 28 34 18 14 27 40 32 43 23 27 0]The non-neutral SFS from SLiM 4.0.0 is
[0 6024 2217 1372 854 556 459 379 365 289 262 221 213 204 165 119 147 143 124 125 104 105 88 93 94 67 67 77 65 74 65 87 72 52 48 51 44 31 57 49 53 41 55 41 43 44 34 31 39 30 45 22 35 39 25 29 27 32 25 27 27 24 13 26 25 22 21 13 18 25 24 14 18 16 18 28 17 28 28 45 13 31 17 17 21 28 15 14 29 17 32 28 20 31 9 19 42 32 27 25 9744]The non-neutral SFS from SLiM 3.7.1 is
[0 6432 2299 1320 916 671 533 453 293 320 275 257 222 197 160 144 154 157 158 112 112 113 82 87 92 86 81 76 63 82 62 76 52 79 64 52 44 49 41 39 50 58 47 51 43 30 36 41 35 46 42 37 29 22 34 18 41 28 26 35 33 32 25 25 28 22 25 38 29 21 20 26 28 43 40 23 17 29 21 20 11 16 23 31 23 18 21 17 31 15 19 30 19 17 13 29 26 32 28 28 9984]So I guess there may be some problems when SLiM 4.0.0 added back neutral mutations with annotation???