-
Notifications
You must be signed in to change notification settings - Fork 31
/
Copy pathModels_3D.py
1032 lines (860 loc) · 44.2 KB
/
Models_3D.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
import numpy
from dadi import Numerics, PhiManip, Integration
from dadi.Spectrum_mod import Spectrum
'''
Models for testing various three population scenarios.
############################################
Daniel Portik
https://github.com/dportik
Updated July 2018
'''
##########################################################################################
#Basic models of (no gene flow / gene flow) between (all / some) population pairs
##########################################################################################
def split_nomig(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3.
Migration does not occur between any population pair.
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
"""
#6 parameters
nu1, nuA, nu2, nu3, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def split_symmig_all(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3.
Migration is symmetrical between all population pairs (ie 1<->2, 2<->3, and 1<->3).
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
"""
#10 parameters
nu1, nuA, nu2, nu3, mA, m1, m2, m3, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def split_symmig_adjacent(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3. Assume 2 occurs
in between populations 1 and 3, which do not come in to contact with one another.
Migration is symmetrical between 'adjacent' population pairs (ie 1<->2, 2<->3, but not 1<->3).
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
"""
#9 parameters
nu1, nuA, nu2, nu3, mA, m1, m2, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
##########################################################################################
#Various models based on forest refugia timing, all with symmetric gene flow estimates
##########################################################################################
def refugia_adj_1(params, ns, pts):
"""
Model with split between pop 1 and (2,3), gene flow does not occur. Split between pops
2 and 3, gene flow does not occur. Period of symmetric secondary contact occurs between
adjacent populations (ie 1<->2, 2<->3, but not 1<->3) after all splits are complete.
'longest isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
T3: The scaled time between the split of pops 2 and 3 and the present (in units of 2*Na generations).
"""
#9 parameters
nu1, nuA, nu2, nu3, m1, m2, T1, T2, T3 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T3, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def refugia_adj_2(params, ns, pts):
"""
Model with split between pop 1 and (2,3), gene flow does not occur. Split between pops
2 and 3, with gene flow. After appearance of 2 and 3, gene flow also occurs between 1
and 2.
'shorter isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#8 parameters
nu1, nuA, nu2, nu3, m1, m2, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def refugia_adj_3(params, ns, pts):
"""
Model with split between pop 1 and (2,3), gene flow does not occur, but then
secondary contact occurs. Split between pops 2 and 3 occurs with gene flow, and gene flow
happens between 1 and 2 as well.
'shortest isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#10 parameters
nu1, nuA, nu2, nu3, mA, m1, m2, T1a, T1b, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1a, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = Integration.two_pops(phi, xx, T1b, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
##########################################################################################
#Various models based on ancient migration and contemporary isolation
##########################################################################################
def ancmig_adj_3(params, ns, pts):
"""
Model with split between pop 1 and (2,3), with gene flow, which then stops. Split
between pops 2 and 3, gene flow does not occur at all.
'longest isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1a: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T1b: The scaled time for no gene flow between pops 1 and (2, 3) (in units of 2*Na generations).
T2: The scaled time between the cessation of gene flow and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#8 parameters
nu1, nuA, nu2, nu3, mA, T1a, T1b, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1a, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = Integration.two_pops(phi, xx, T1b, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def ancmig_adj_2(params, ns, pts):
"""
Model with split between pop 1 and (2,3), with gene flow. Split
between pops 2 and 3, and all gene flow ceases.
'shorter isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#7 parameters
nu1, nuA, nu2, nu3, mA, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def ancmig_adj_1(params, ns, pts):
"""
Model with split between pop 1 and (2,3), with gene flow. Split
between pops 2 and 3 with gene flow, then all gene flow ceases.
'shortest isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 and present (in units of 2*Na generations).
"""
#10 parameters
nu1, nuA, nu2, nu3, mA, m1, m2, T1, T2, T3 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T3, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
##########################################################################################
#### Simultaneous split models (with/without migration/secondary contact and size changes)
#### Written for Barratt et al. (2018)
##########################################################################################
def sim_split_no_mig(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3, gene flow does not occur.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
T1: The scaled time between the split and the present (in units of 2*Na generations).
"""
#4 parameters
nu1, nu2, nu3, T1 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def sim_split_no_mig_size(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3, gene flow does not occur, but size change does.
nu1a: Size of population 1 after split.
nu2a: Size of population 2 after split.
nu3a: Size of population 3 after split.
nu1b: Size of population 1 after size change.
nu2b: Size of population 2 after size change.
nu3b: Size of population 3 after size change.
T1: The scaled time between the split and the size change (in units of 2*Na generations).
T2: The scaled time between the size change and present.
"""
#8 parameters
nu1a, nu2a, nu3a, nu1b, nu2b, nu3b, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1a, nu2=nu2a, nu3=nu3a, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1b, nu2=nu2b, nu3=nu3b, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def sim_split_sym_mig_all(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3
Migration is symmetrical between all population pairs (ie 1<->2, 2<->3, and 1<->3).
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split and the present (in units of 2*Na generations).
"""
#7 parameters
nu1, nu2, nu3, m1, m2, m3, T1 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def sim_split_sym_mig_adjacent(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3
Migration is symmetrical between 'adjacent' population pairs (ie 1<->2, 2<->3, but not 1<->3).
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split and the present (in units of 2*Na generations).
"""
#6 parameters
nu1, nu2, nu3, m1, m2, T1 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def sim_split_refugia_sym_mig_all(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3 followed by isolation. Period of
symmetric secondary contact occurs between all populations after all splits are complete.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split and the present (in units of 2*Na generations).
T2: The scaled time between the migration (secondary contact) and the present (in units of 2*Na generations).
"""
#8 parameters
nu1, nu2, nu3, m1, m2, m3, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def sim_split_refugia_sym_mig_adjacent(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3 followed by isolation. Period of
symmetric secondary contact occurs between adjacent populations (ie 1<->2, 2<->3, but
not 1<->3) after all splits are complete.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split and the present (in units of 2*Na generations).
T2: The scaled time between the migration (secondary contact) and the present (in units of 2*Na generations).
"""
#7 parameters
nu1, nu2, nu3, m1, m2, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
###############################################################
#### Models with extra size change step (potential human impact)
#### Written for Barratt et al. (2018)
###############################################################
def split_nomig_size(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3.
Migration does not occur between any population pair, size change
nu1a: Size of population 1 after split.
nuA: Size of ancestral population (pops 2 and 3)
nu2a: Size of population 2 after split.
nu3a: Size of population 3 after split.
nu1b: Size of population 1 after size change.
nu2b: Size of population 2 after size change.
nu3b: Size of population 3 after size change.
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
T3: The scaled time between the size change and the present (in units of 2*Na generations).
"""
#10 parameters
nu1a, nuA, nu2a, nu3a, nu1b, nu2b, nu3b, T1, T2, T3 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1a, nuA, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1a, nu2a, nu3a, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T3, nu1b, nu2b, nu3b, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def ancmig_2_size(params, ns, pts):
"""
Model with split between pop 1 and (2,3), with gene flow. Split
between pops 2 and 3, and all gene flow ceases, then size change
shorter isolation
nu1a: Size of population 1 after split.
nuA: Size of ancestral population (pops 2 and 3)
nu2a: Size of population 2 after split.
nu3a: Size of population 3 after split.
nu1b: Size of population 1 after size change.
nu2b: Size of population 2 after size change.
nu3b: Size of population 3 after size change.
mA: Migration rate between pops 1 and (2 and 3)
T1: The scaled time between the split of pops 1 vs 2 and 3 (ancient migration)(in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
T3: The scaled time between the size change and the present (in units of 2*Na generations).
"""
#11 parameters
nu1a, nuA, nu2a, nu3a, nu1b, nu2b, nu3b, mA, T1, T2, T3 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1a, nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1a, nu2a, nu3a, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T3, nu1b, nu2b, nu3b, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def sim_split_refugia_sym_mig_adjacent_size(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3 followed by isolation. Period of
symmetric secondary contact occurs between adjacent populations (ie 1<->2, 2<->3, but
not 1<->3) after all splits are complete, and a size change.
nu1a: Size of population 1 after split.
nu2a: Size of population 2 after split.
nu3a: Size of population 3 after split.
nu1b: Size of population 1 after size change.
nu2b: Size of population 2 after size change.
nu3b: Size of population 3 after size change.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations) (in units of 2*Na generations).
T2: The scaled time between the split and the migration (secondary contact) (in units of 2*Na generations).
T3: The scaled time between the size change and the present (in units of 2*Na generations).
"""
#11 parameters
nu1a, nu2a, nu3a, nu1b, nu2b, nu3b, m1, m2, T1, T2, T3 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1a, nu2a, nu3a, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T2, nu1a, nu2a, nu3a, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T3, nu1b, nu2b, nu3b, m12=m1, m21=m1, m23=m2, m32=m2, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
###############################################################
#### Variation on divergence, with pop3 geographically between
#### pop1 and pop2
#### Written for Firneno et al. (2020)
###############################################################
#but with pop 3 treated as 'middle' population
def refugia_adj_2_var_sym(params, ns, pts):
"""
Model with split between pop 1 and (2,3), gene flow does not occur. Split between pops
2 and 3, with gene flow. After appearance of 2 and 3, gene flow also occurs between 1
and 3.
'shorter isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#8 parameters
nu1, nuA, nu2, nu3, m2, m3, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def refugia_adj_2_var_uni(params, ns, pts):
"""
Model with split between pop 1 and (2,3), gene flow does not occur. Split between pops
2 and 3. Gene flow from pop1 to pop3 (unidirectional), and from pop2 to pop3 (unidirectional).
'shorter isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m32: Migration rate from pop 2 to pop3 (2*Na*m)
m31: Migration rate from pop 1 to pop3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#8 parameters
nu1, nuA, nu2, nu3, m32, m31, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=m32, m13=0, m31=m31)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def refugia_adj_3_var_sym(params, ns, pts):
"""
Model with split between pop 1 and (2,3), gene flow does not occur, but then
secondary contact occurs. Split between pops 2 and 3 occurs with gene flow, and gene flow
happens between 1 and 3 as well.
'shortest isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#10 parameters
nu1, nuA, nu2, nu3, mA, m2, m3, T1a, T1b, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1a, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = Integration.two_pops(phi, xx, T1b, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def refugia_adj_3_var_uni(params, ns, pts):
"""
Model with split between pop 1 and (2,3), gene flow does not occur, but then
secondary contact occurs. Gene flow from pop1 to pop3 (unidirectional), and
from pop2 to pop3 (unidirectional).
'shortest isolation'
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m32: Migration rate from pop 2 to pop3 (2*Na*m)
m31: Migration rate from pop 1 to pop3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the first split and the split of pops 2 and 3 (in units of 2*Na generations).
"""
#10 parameters
nu1, nuA, nu2, nu3, mA, m32, m31, T1a, T1b, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1a, nu1=nu1, nu2=nuA, m12=0, m21=0)
phi = Integration.two_pops(phi, xx, T1b, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=m32, m13=0, m31=m31)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def split_sym_mig_adjacent_var1(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3.
Migration is symmetrical between 'adjacent' population pairs (ie 1<->3, 2<->3, but not 1<->2).
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
"""
#9 parameters
nu1, nuA, nu2, nu3, mA, m2, m3, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def split_uni_mig_adjacent_var1(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3.
Gene flow from pop1 to pop3 (unidirectional), and from pop2 to pop3 (unidirectional).
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m32: Migration rate from pop 2 to pop3 (2*Na*m)
m31: Migration rate from pop 1 to pop3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
"""
#9 parameters
nu1, nuA, nu2, nu3, mA, m32, m31, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=m32, m13=0, m31=m31)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def split_sym_mig_adjacent_var2(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3.
Migration is symmetrical between pop 1 and pop(2,3), then between pop1 and pop3 only.
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
"""
#8 parameters
nu1, nuA, nu2, nu3, mA, m3, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def split_uni_mig_adjacent_var2(params, ns, pts):
"""
Model with split between pop 1 and (2,3), then split between 2 and 3.
Migration is symmetrical between pop 1 and pop(2,3), then from pop1 to pop3 (unidirectional).
nu1: Size of population 1 after split.
nuA: Size of population (2,3) after split from 1.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
mA: Migration rate between population 1 and population (2,3)
m31: Migration rate from pop 1 to pop3
T1: The scaled time between the split of pops 1 vs 2 and 3 (in units of 2*Na generations).
T2: The scaled time between the split of pops 2 and 3 (in units of 2*Na generations).
"""
#8 parameters
nu1, nuA, nu2, nu3, mA, m31, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nuA, m12=mA, m21=mA)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=m31)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
###############################################################
#### Variation on simultaneous split models, with pop3
#### geographically between pop1 and pop2
#### Written for Firneno et al. (2020)
###############################################################
#but with pop 3 treated as 'middle' population
def sim_split_sym_mig_adjacent_var(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3
Migration is symmetrical between 'adjacent' population pairs (ie 1<->3, 2<->3, but not 1<->2).
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split and the present (in units of 2*Na generations).
"""
#6 parameters
nu1, nu2, nu3, m2, m3, T1 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def sim_split_uni_mig_adjacent_var(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3
Gene flow from pop1 to pop3 (unidirectional), and from pop2 to pop3 (unidirectional).
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m32: Migration rate from pop 2 to pop3 (2*Na*m)
m31: Migration rate from pop 1 to pop3
T1: The scaled time between the split and the present (in units of 2*Na generations).
"""
#6 parameters
nu1, nu2, nu3, m32, m31, T1 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=m32, m13=0, m31=m31)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def sim_split_refugia_sym_mig_adjacent_var(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3 followed by isolation. Period of
symmetric secondary contact occurs between adjacent populations (ie 1<->3, 2<->3, but
not 1<->2) after all splits are complete.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m1: Migration rate between populations 1 and 2 (2*Na*m)
m2: Migration rate between populations 2 and 3
m3: Migration rate between populations 1 and 3
T1: The scaled time between the split and the present (in units of 2*Na generations).
T2: The scaled time between the migration (secondary contact) and the present (in units of 2*Na generations).
"""
#7 parameters
nu1, nu2, nu3, m2, m3, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
#but with pop 3 treated as 'middle' population
def sim_split_refugia_uni_mig_adjacent_var(params, ns, pts):
"""
Model with simultaneous split between pop 1, 2 and 3 followed by isolation. After all
splits are complete, gene flow from pop1 to pop3 (unidirectional), and from pop2 to
pop3 (unidirectional).
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after split.
m32: Migration rate from pop 2 to pop3 (2*Na*m)
m31: Migration rate from pop 1 to pop3
T1: The scaled time between the split and the present (in units of 2*Na generations).
T2: The scaled time between the migration (secondary contact) and the present (in units of 2*Na generations).
"""
#7 parameters
nu1, nu2, nu3, m32, m31, T1, T2 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = PhiManip.phi_2D_to_3D_split_2(xx, phi)
phi = Integration.three_pops(phi, xx, T1, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=m32, m13=0, m31=m31)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
###############################################################
#### Admixed ("hybrid") origin models
#### Written for Firneno et al. (2020)
###############################################################
def admix_origin_no_mig(params, ns, pts):
"""
Model with split between pop 1 and 2, gene flow does not occur.
Population 3 is admixed from pop 1 and 2, no gene flow occurs.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after origin.
T1: The scaled time between the split of pops 1 vs 2 and origin of 3 (in units of 2*Na generations).
T2: The scaled time between the origin of pop 3 and the present (in units of 2*Na generations).
f: Fraction of pop 3 derived from pop 1 (with fraction 1-f derived from pop 2).
"""
#6 parameters
nu1, nu2, nu3, T1, T2, f = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nu2, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_admix(phi, f, xx, xx, xx)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=0, m32=0, m13=0, m31=0)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))
return fs
def admix_origin_sym_mig_adj(params, ns, pts):
"""
Model with split between pop 1 and 2, gene flow does not occur.
Population 3 is admixed from pop 1 and 2.
Gene flow between pop1 and pop3, and between pop2 and pop3.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
nu3: Size of population 3 after origin.
m3: Migration rate between populations 1 and 3 (2*Na*m)
m2: Migration rate between populations 2 and 3
T1: The scaled time between the split of pops 1 vs 2 and origin of 3 (in units of 2*Na generations).
T2: The scaled time between the origin of pop 3 and the present (in units of 2*Na generations).
f: Fraction of pop 3 derived from pop 1 (with fraction 1-f derived from pop 2).
"""
#8 parameters
nu1, nu2, nu3, m2, m3, T1, T2, f = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T1, nu1=nu1, nu2=nu2, m12=0, m21=0)
phi = PhiManip.phi_2D_to_3D_admix(phi, f, xx, xx, xx)
phi = Integration.three_pops(phi, xx, T2, nu1=nu1, nu2=nu2, nu3=nu3, m12=0, m21=0, m23=m2, m32=m2, m13=m3, m31=m3)
fs = Spectrum.from_phi(phi, ns, (xx,xx,xx))