Supplementary Information
Gga1, case 1: a fission event
In chicken, ETNK1 and PTMS are located on each side of the centromere, at positions 68.6
and 80.3 Mb, respectively, and separated by a genetic distance of 33 cM. In collared
flycatcher, they form the respective ends of the linkage groups Fal3 and Fal8. Cytogenetic
analysis has identified a fission event in this region in three other passerine bird families
(DERJUSHEVA et al. 2004; GUTTENBACH et al. 2003; ITOH and ARNOLD 2005), and it thus
seem likely that it arose early in the evolution of Passeriformes. An independent fission event
in the same region has been seen in eagle owl (Bubo bubo) (GUTTENBACH et al. 2003).
Gga1, case 2: a possible fission event
In chicken, ENSGALT00000025613 and ATP6AP2 are only 7.4 Mb apart (at 108.5 and 115.9
Mb, respectively). In collared flycatcher, they form the respective ends of linkage groups Fal4
and Fal8. Recombination in this region is at unusually high rate in chicken (46 cM in 4.5
Mb). If a recombination hot spot of a similar magnitude is located in this region also in
collared flycatcher, then we are unlikely to be able to connect linkage groups Fal4 and Fal8.
The degree of conservation of the recombinational landscape along avian chromosomes is not
known, although we note that in mammals there is a fast turnover of recombination hotspots
(PTAK et al. 2005; PTAK et al. 2004; SPENCER et al. 2006). Failure to detect linkage between
Fal4 and Fal8 could potentially also be due to a large insertion in this region of the flycatcher
genome. Of course, it is also possible that it represents a true fission event in the lineage
leading to collared flycatcher.
Gga3: a possible fission/fusion event
Both linkage groups Fal22 and Fal2 in collared flycatcher correspond to chicken
chromosome 3. The markers flanking the gap, LHCGR and TGFB2, are separated by 13.0 Mb
in chicken, or 45 cM. This probably indicates that the gap is a result of lack of power to detect
linkage over such a long physical/genetic distance.
Gga4: a fusion event
Two collared flycatcher linkage groups (Fal15 and Fal18) correspond to chicken
chromosome 4 and this represents a well-known fusion event in the lineage leading to chicken
subsequent to its split from the lineage leading to turkey (REED et al. 2005). It is detected in
almost all cytogenetic comparisons of chicken and other birds (GRIFFIN et al. 2007).
However, a similar fusion event has happened independently in the lineage leading to graylag
goose (Anser anser) within Anseriformes (GRIFFIN et al. 2007) so this chromosomal region
seems to contain fragile sites for genomic rearrangement.
Gga8: a possible fission/fusion event
There are two collared flycatcher linkage groups (Fal9 and Fal11) matching up to chicken
chromosome 8. Gene orders suggest that there has been an inversion event in either lineage,
and it therefore difficult to assess whether an interchromosomal rearrangement also has taken
place.
Gga12: a possible fusion/fission event
Linkage groups Fal21 and Fal31 in collared flycatcher correspond to chicken chromosome
12. The markers flanking the gap, PSMD6 and THUMPD3, are separated by no more than 6.2
Mb in chicken, or 23 cM. Unless recombination is significantly elevated in this region in
collared flycatchers or there has been a substantial insertion, this may demark a fission event
in the lineage leading to collared flycatcher.
Gga14: a possible fusion/fission event
Linkage groups Fal28 and Fal32 in collared flycatcher correspond to chicken chromosome
14. The markers flanking the gap, C7orf27 and 12630, are separated by 10.0 Mb in chicken,
or 29 cM. It is difficult to judge whether this indicates a fission event or failure to detect
linkage.
Fal30: a possible fusion/fission event
RL13 is linked to a single microsatellite marker (EST46) in collared flycatcher but shows no
linkage to markers on chicken chromosome 11, where it is located in that species. RL13 is
10.0 Mb away from the next marker (07726) on Gga11, close to 11q, and has rather limited
number of informative meiosis. The lack of evidence for linkage between RL13 and other
markers from Gga11 in collared flycatcher may be most likely explained by a lack of power.
Fal33: a possible fusion/fission event
Fal33 consists of two gene markers, NAT5 and NDUFA7. These markers are supposed to
have their orthologs on chicken chromosome 7 and 28, respectively. However, NDUFA7 has
a low BLAST hit score to Gga28 (BACKSTRÖM et al. 2008) so it may not represent the true
orthologue NAT5 is the outmost marker on Gga7, very close to the terminus, and there may be
a lack of power to detect linkage to other markers from Gga7/Fal7.
Supplementary Table 1. Pedigree structure of collared flycatchers used for linkage
mapping.
Pedigree
Subject Sex
Father
Mother
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
3
1
400
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
401
34
35
36
37
38
39
40
41
42
U
U
1
1
1
1
1
U
1
1
1
1
1
1
1
U
1
1
1
1
1
U
U
21
21
21
21
21
21
U
21
21
21
U
U
33
33
U
33
33
33
U
33
33
U
U
400
400
400
400
400
U
7
7
7
7
7
7
7
U
15
15
15
15
15
U
U
22
22
22
22
22
22
U
29
29
29
U
U
401
401
U
36
36
36
U
40
40
M
F
U
U
U
U
U
F
U
U
U
U
U
U
U
F
U
U
U
U
U
M
F
U
U
U
U
U
U
F
U
U
U
M
F
U
U
F
U
U
U
F
U
U
3
3
4
4
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
5
5
5
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
7
7
7
7
7
7
7
43
44
45
46
47
48
49
50
51
53
54
55
56
58
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
U
U
M
F
U
U
F
U
U
F
U
U
U
U
M
F
U
U
U
U
F
U
U
U
U
U
U
M
F
U
U
U
U
U
U
U
F
U
U
U
U
U
U
M
F
U
U
U
U
U
33
33
U
U
45
45
U
45
45
U
45
45
45
45
U
U
61
61
61
61
U
61
61
61
61
61
61
U
U
74
74
74
74
74
74
74
U
74
74
74
74
74
74
U
U
90
90
90
90
90
40
40
U
U
46
46
U
49
49
U
53
53
53
53
U
U
62
62
62
62
U
67
67
67
67
67
67
U
U
75
75
75
75
75
75
75
U
83
83
83
83
83
83
U
U
91
91
91
91
91
7
7
7
7
7
7
7
7
7
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
9
9
9
9
9
9
9
9
9
9
9
9
9
10
10
10
10
10
10
10
10
10
10
10
10
10
97
98
99
100
101
102
103
104
105
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
402
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
148
U
F
U
U
U
U
U
U
F
M
F
U
U
U
U
U
F
U
F
U
U
U
U
U
M
F
U
U
U
U
U
F
U
U
U
U
U
M
F
U
U
U
U
U
F
U
U
U
F
U
90
U
90
90
90
90
90
90
U
U
U
107
107
107
107
107
U
107
U
107
107
107
107
107
U
U
122
122
122
122
122
U
122
122
122
122
122
U
U
134
134
134
134
134
U
134
134
134
U
134
91
U
98
98
98
98
98
98
U
U
U
108
108
108
108
108
U
114
U
116
116
116
116
116
U
U
123
123
123
123
123
U
402
402
402
402
402
U
U
135
135
135
135
135
U
141
141
141
U
145
10
10
11
11
11
11
11
11
11
11
11
11
11
11
11
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
13
14
14
14
14
14
14
14
14
14
14
14
14
14
151
152
153
154
155
156
157
158
159
160
161
162
163
165
166
404
180
181
182
183
186
167
173
174
175
176
177
178
180
184
185
187
189
190
192
193
194
195
196
197
198
199
202
203
204
205
206
207
208
209
U
U
M
F
U
U
F
U
U
F
U
U
F
U
U
M
F
U
U
U
U
M
F
U
U
U
U
U
F
U
U
F
U
U
U
U
U
M
F
U
U
U
U
F
U
U
U
U
U
U
134
134
U
U
153
153
U
153
153
U
153
153
U
153
153
U
U
404
404
404
404
U
U
167
167
167
167
167
U
167
167
U
167
167
167
167
167
U
U
195
195
195
195
U
195
195
195
195
195
195
145
145
U
U
154
154
U
157
157
U
160
160
U
163
163
U
U
180
180
180
180
U
U
173
173
173
173
173
U
180
180
U
187
187
187
187
187
U
U
196
196
196
196
U
203
203
203
203
203
203
14
14
14
14
14
14
15
15
15
15
15
15
15
15
15
17
17
17
17
17
17
17
17
17
17
18
18
18
18
18
18
18
18
18
18
18
18
18
18
18
18
18
18
18
19
19
19
19
19
19
210
211
212
214
216
217
219
220
221
222
223
225
226
227
234
265
266
269
270
271
272
273
274
278
279
283
284
285
286
287
288
290
291
292
293
294
295
296
297
298
299
300
301
303
304
305
306
307
308
309
U
F
U
U
U
U
M
F
U
U
U
U
U
F
F
M
F
U
U
U
U
U
F
U
U
M
F
U
U
U
U
F
U
U
U
U
U
U
U
F
U
U
U
U
M
F
U
U
U
U
195
U
195
195
195
195
U
U
219
219
219
219
219
U
U
U
U
265
265
265
265
265
U
265
265
U
U
283
283
283
283
U
283
283
283
283
283
283
283
U
283
283
283
283
U
U
304
304
304
304
203
U
211
211
211
211
U
U
220
220
220
220
220
U
U
U
U
266
266
266
266
266
U
274
274
U
U
284
284
284
284
U
290
290
290
290
290
290
290
U
298
298
298
298
U
U
305
305
305
305
19
19
19
19
19
20
20
20
20
20
20
20
20
20
20
20
21
21
21
21
21
21
21
21
21
21
22
22
22
22
22
22
22
22
22
22
16
16
16
16
16
16
16
16
16
16
16
16
16
16
310
405
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
406
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
354
355
356
357
358
359
360
361
U
F
U
U
U
M
F
U
U
U
U
U
U
F
U
U
M
F
U
U
U
F
U
U
U
U
M
F
U
U
F
U
U
U
F
U
M
F
U
U
U
U
F
U
U
U
U
U
U
U
304
U
304
304
304
U
U
314
314
314
314
314
314
U
314
314
U
U
325
325
325
U
325
325
325
325
U
U
334
334
U
334
334
334
U
334
U
U
344
344
344
344
U
344
344
344
344
344
344
344
305
U
405
405
405
U
U
315
315
315
315
315
315
U
322
322
U
U
406
406
406
U
329
329
329
329
U
U
335
335
U
338
338
338
U
342
U
U
345
345
345
345
U
354
354
354
354
354
354
354
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
16
362
363
364
365
366
367
368
242
243
244
245
246
247
248
249
250
251
252
253
254
257
258
259
260
261
262
263
264
M
F
U
U
U
U
U
M
F
U
U
U
U
U
U
U
F
U
U
U
U
F
U
U
U
U
U
U
344
U
362
362
362
362
362
U
U
242
242
242
242
242
242
242
344
242
242
242
242
U
242
242
242
242
242
242
345
U
363
363
363
363
363
U
U
243
243
243
243
243
243
243
345
251
251
251
251
U
258
258
258
258
258
258
Supplementary Table 2. Number of informative meioses for collared flycatcher markers
and the closest marker on the chicken genetic linkage map (from
http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031).
Gene marker name
# Informative meiosis
Genetic marker, chicken
00548
02079
02419
04550
05087
07726
08235
08544
12630
15691
15738
17140
18798
20352
20904
21277
22644
25613
25924
27425
27623
ABHD10
ACADL
ACADSB
ACHA9
ACLY
ACOT8
ACTB
ADAL
ADH5
ADIPOR1
ALAS1
AN32B
ANAPC5
ANKRD49
ARF1
ARHGEF9
ARHL2
ARP6
ASB6
ATG4B
ATP6AP2
64
157
123
157
246
271
248
126
30
266
127
253
184
222
245
171
88
257
163
270
220
219
192
252
103
213
178
123
229
248
154
206
226
225
219
240
68
256
205
218
151
255
n.a
MCW0228
ADL0206
MSU0037
MCW0278
ROS0111
n.a
MCW0375
MCW0123
ADL0312
MCW0114
n.a
ACW0309
MCW0062
ABR0051
ADL0181
MSU0432
MSU0028
LEI0340
ACW0308
n.a
MCW0068
ACW0299
ABR0323
MSU0405
ADL0376
LEI0346
MCW0228
ADL0038
ABR0331
MCW0356
ROS0274
no marker
LEI0120
UMA1.003
ABR0020
ACW0311
LEI0090
ROS0058
ADL0149
ADL0191
ROS0081
ATP6V1E1
BZW1
C12orf29
C7orf27
C8orf53
CACYBP
CATB
CBPZ
CCDC104
CCDC132
CCDC137
CCNG1
CCT2
CDH9
CEPU1
CGI-62
CHC
CHD1L
CHM1B
CHMP5
CNTN1
COEA1
CRIPT
CT030
DC1L1
DDAH1
DECR1
DLD
DPYSL3
DST
EDF1
EF1A1
EF1A
EIF3S1
ENO1
ETNK1
FAK1
FN
FTH
GAS7
GH1
GNB1
GTF2B
HARS
HEPACAM
HMGB2
HMGN2
IGF2R
IGFBP7
KCNIP4
295
44
75
150
280
247
197
244
211
94
211
227
161
166
208
105
91
192
222
155
227
240
277
197
251
110
295
67
12
256
41
72
184
224
135
222
251
284
250
57
155
142
222
16
199
258
96
187
211
14
LEI0174
MCW0120
MGFsts1
ADL0200
ACW0284
MCW0275
ACW0170
LEI0063
MCW261
n.a
n.a
ACW0167
HUJ0003
VPI0001
ROS0113
ADL0271
C1QBPsts1
ROS0353
GCT0026
ACW002
MCW0386
LEI0228
ACW0257
n.a
ACW0467
ACW0417
MCW0310
SCW0048
MCW0104
ACW0326
ACW0117
ADL0306
ROS0265
ABR0012
ROS0133
MCW0007
ADL0146
ACW0299
n.a
n.a
MCW0313
AGRNsts1
MCW0160
ACW0433
MCW0075
MSU0055
LEI0352
MSU0402
OC-116sts1
MCW0122
KCRB
KIAA1706
LARP1
LDHA
LHCGR
MAGOH
MBP
METRNL
MIC1
MITD1
MMAA
MOSPD2
MPP1
MPP6
MRPS18A
NAT5
NDST3
NDUFA7
NSMAF
NY-SAR-48
OAZ
ODC11
PARK7
PDCD11
PDHL1
PES1
PKHB2
PNN
POLR2C
POLR2H
PPIL4
PRS4
PSMB1
PSMC2
PSMC3
PSMC5
PSMD14
PSMD6
PTMS
RAB12
RAB3GAP1
RABL4
RASGEF1A
RBBP7
RBM18
RBM26
RHO
RL13
RNASEH1
ROBO1
199
58
229
105
206
195
266
14
261
287
170
243
135
243
207
189
241
157
202
248
237
186
239
224
291
164
232
108
232
214
158
193
190
249
125
146
212
273
213
204
134
183
257
238
63
239
256
75
163
99
ACW0309
ACW0211
MSU0379
COM0015
MSU0360
MSU0302
MSU0478
n.a
ROS0023
LEI0169
ACW0272
SCW0043
n.a
MCW0131
ACW0193
ADL0169
MCW0284
n.a
PENKsts1
ROS0251
ABR0341
MSU0053
CDC2L1sts1
ACW0418
SCW0043
MSU0032
COM0128
ACW0419
LEI0143
NCLsts1
MSU0447
MCW0113
ACW0468
SCW0048
ROS0323
LEI0350
ACW0361
GCT0055
ACW0234
LEI0147
LEI0158
ACW0290
MSU430
ABR0085
MCW0335
MCW0381
MSU0490
n.a
MCW0006
MCW0195
RPL5
RPL7A
RPL11
RPL23
RPL30
RPL37A
SBDS
SERINC1
SPCS1
STYX
TGFB2
THUMPD3
TIMM17A
TM
TMEM32
TUBGCP3
TXNDC14
UBE2J1
UCHL3
UCHL5
UQCRC1
VIPR2
VISL1
VPS26A
WDR24
YME1L1
YPEL5
EST9
EST10
EST16
EST31
EST46
GG-C25
ZF-C59
ZF-S8
ZF-S9
Fhy223
Fhy224
Fhy230
Fhy235
Fhy236
Fhy301
Fhy326
Fhy329
Fhy344
Fhy350
Fhy356
Fhy361
Fhy370
Fhy407
246
146
175
216
154
261
314
199
219
173
160
182
113
68
228
268
1
219
198
140
178
207
6
252
267
116
59
339
240
245
316
255
285
234
326
329
304
259
295
290
329
58
221
246
241
121
244
145
122
254
ADL0171
HUJ0002
LEI0014
ADL0376
MCW0245
MCW0183
SCYA4sts1
ROS0349
ADL0372
KCRB160
ARHGDIGsts1
MSU0490
MCW0355
ADL0209
ABR0042
MCW0049
MCW0193
ROS0119
MCW0177
ROS0338
MSU320
COM0098
ADL0237
MSU0303
ACW0384
ADL0190
ADL0177
ACW0418
ACW0418
ACW0395
LEI0179
ADL0033
MCW0078
ACW0395
n.a
ROS0325
ADL0314
MCW0031
ACW0178
ACW0459
HCKsts1
MSU0007
ACW0347
ADL0371
LEI0063
MCW0052
GCT0050
ACW0206
ADL0367
COM0129
Fhy415
Fhy427
Fhy453
Fhy458
Fhy465
Fhy466
290
164
185
164
236
256
MCW0291
MSU0011
COM0075
MCW0310
COM0129
ACW0101