Supplementary material, Table 1: Thermocycling conditions for all microsatellite loci used to individually
identify humpback whales from Antarctic Whale Expedition, eastern and western Australia, Australian
Marine Mammal Center dataset. PCR conditions are detailed in Schmitt et al. (In Press).
Loci
Label
Multiplex group
Size range
Ev1
N alleles
VIC
Set 3
123 – 129
4
Ev14
VIC
Set 2
125 – 145
9
Ev37
NED
Set 1
192 – 230
21
Ev94
FAM
Set 3
202 – 220
9
Ev96
FAM
Set 2
147 – 173
13
GATA 417
FAM
Set 2
183 – 282
17
GT 211
FAM
Individually
98 – 120
10
GT 23
VIC
Set 1
101 – 123
9
GT 575
VIC
Set 3
137 – 177
15
rw4-10
VIC
Individually
192 – 216
13
dlp
See Olavarría et al. (2007) for method details
sex
See Morin et al. (2005) for method details
Schmitt NT, Double MC, Jarman SN, Gales N, Marthick JR, Polanowski AM, Baker CS, Steel D, Jenner
KCS, Jenner M-NM, Gales R, Paton D, Peakall R (In Press) Low levels of genetic differentiation
characterize Australian humpback whale (Megaptera novaeangliae) populations. Mar Mamm Sci doi:
10.1111/mms.12045
Olavarría C. Baker CS, Garrigue C, Poole M, Hauser N, Caballero S, Flórez-González L, Brasseur M,
Bannister J, Capella J, Clapham P, Dodemont R, Donoghue M, Jenner C, Jenner M-N, Moro D,
Oremus M, Paton D, Rosenbaum H, Russell K (2007) Population structure of South Pacific
humpback whales and the origin of the Eastern Polynesian breeding grounds. Mar Ecol Prog Series
330:257-268
Morin PA, Nestler A, Rubio-Cisneros NT, Robertson KM, Mesnick SL (2005) Interfamilial
characterization of the ZFX and ZFY genes facilitates sex determination in cetaceans and other
mammals. Mol Ecol 14:3275-3286
Supplementary material, Table 2: Thermocycling conditions for microsatellite loci used to individually identify humpback whales from Oceania
and the Antarctic, South Pacific Whale Research Consortium dataset. PCR profile listed is for 96-well format, an extra 5 cycles were added for
384 well format PCRs. Further details can be found in Steel et al. (2008).
Loci
Ev1
Ev14
Ev37
Ev94
Ev96
GATA 417
GT 211
GT 23
GT 575
rw4-10
dloop
sex
Co-load
Size range N
[Mg2+]
group
alleles
(mM)
NED
1
123 – 129
4
4
VIC
1
125 – 145
10
2.5
NED
3
192 – 230
20
3.5
FAM
3
202 – 220
9
2.5
FAM
3
147 – 173
12
1.5
FAM
2
183 – 282
23
2.5
FAM
2
98 – 120
12
2.5
VIC
4
101 – 123
9
2.5
FAM
2
137 – 177
12
1.5
VIC
2
192 – 216
12
3
See Olavarría et al. (2007) for method details
See Olavarría et al. (2007) for method details
Label
PCR Profile
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 30sec) x35, 72oC 10min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 40sec) x35, 72oC 30min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 30sec) x35, 72oC 10min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 40sec) x35, 72oC 30min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 40sec) x35, 72oC 30min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 40sec) x35, 72oC 30min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 30sec) x35, 72oC 10min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 40sec) x35, 72oC 30min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 30sec) x35, 72oC 10min
94oC 3min, (94oC 30sec, 50oC 30sec, 72oC 30sec) x35, 72oC 10min
Steel D, Garrigue C, Poole M, Hauser N, Olavarría C, Flórez-González L, Constantine R, Caballero S, Thiele D, Paton D, Clapham P, Donoghue
M, Baker CS (2008) Migratory connections between humpback whales from South Pacific breeding grounds and Antarctic feeding areas
based on genotype matching. Report (SC/60/SH13) to the Scientific Committee of the International Whaling Commission, Santiago, Chile.
Olavarría C. Baker CS, Garrigue C, Poole M, Hauser N, Caballero S, Flórez-González L, Brasseur M, Bannister J, Capella J, Clapham P,
Dodemont R, Donoghue M, Jenner C, Jenner M-N, Moro D, Oremus M, Paton D, Rosenbaum H, Russell K (2007) Population structure of
South Pacific humpback whales and the origin of the Eastern Polynesian breeding grounds. Mar Ecol Prog Series 330:257-268
Supplementary material, Table 3: Thermocycling conditions for microsatellite loci used to individually identify humpback whales from eastern
Australia, Southern Cross University dataset. Further details can be found in Anderson et al. (2010).
Loci
Label
Ev1
[Mg2+] PCR Profile
(mM)
2
92ºC 1min, (92ºC 10sec, 59ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
Size range
TET
Co-load
group
2
119 – 125
N
alleles
4
Ev14*
HEX
1
126 – 144
9
3.5
92ºC 1min, (92ºC 10sec, 66ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
Ev37*
TET
1
163 – 205
22
3.5
92ºC 1min, (92ºC 10sec, 56ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
Ev94*
HEX
1
182 – 204
11
3.5
92ºC 1min, (92ºC 10sec, 60ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
Ev96*
FAM
1
146 – 172
13
2
92ºC 1min, (92ºC 10sec, 66ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
GATA 417* FAM
1
216 – 316
18
2
92ºC 1min, (92ºC 10sec, 60ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
GT 211
FAM
2
192 – 212
10
1.5
92ºC 1min, (92ºC 10sec, 58ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
GT 575
FAM
2
134 – 174
15
2
92ºC 1min, (92ºC 10sec, 56ºC 30sec, 75ºC 1min) x 35, 75ºC 5min, 30ºC 1min
dloop
sex
See Olavarría et al (2007) for method details
See Olavarría et al (2007) for method details
Anderson M, Steel D, Franklin W, Franklin T, Paton D, Burns D, Harrison P, Baverstock P, Garrigue C, Olavarría C, Poole MM, Hauser N,
Constantine R, Thiele D, Clapham P, Donoghue M, Baker CS (2010) Microsatellite genotype matches of eastern Australian humpback whales
to Area V feeding and breeding grounds. IWC Scientific Committee Document SC/62/SH7. Available from the International Whaling
Commission
Olavarría C. Baker CS, Garrigue C, Poole M, Hauser N, Caballero S, Flórez-González L, Brasseur M, Bannister J, Capella J, Clapham P,
Dodemont R, Donoghue M, Jenner C, Jenner M-N, Moro D, Oremus M, Paton D, Rosenbaum H, Russell K (2007) Population structure of
South Pacific humpback whales and the origin of the Eastern Polynesian breeding grounds. Mar Ecol Prog Series 330:257-268
Supplementary material Table 4: Summary of matching microsatellite genotypes for humpback whales sampled in Antarctic feeding Area V (n =
57) and the migratory corridors and breeding grounds of Oceania and Australia (n = 2,272). -/- indicate an amplification failure at that locus for
that sample. Blank cells indicate that a sample was not run for that locus for one of the three datasets.
Sample Name
Location
Date
dlp
sex
Ev1
Ev14
Ev37
Ev94
Ev96
GATA 417
GT 211
GT 23
GT 575
rw 4-10
2010AWE014
Area V
1 Mar 10
SP11
F
123/125
131/137
198/214
212/212
161/163
199/222
106/118
109/115
151/151
204.206
Mn463
Hervey Bay
11 Oct 00
-
F
123/125
131/137
198/214
212/212
161/163
199/222
106/118
2010AWE204
Area V
21 Feb 10
SP3
M
123/123
131/139
212/214
212/214
171/173
214/222
106/106
Mn658
Byron Bay
2004
-
M
123/123
131/139
212/214
212/214
-/-
214/222
106/106
2010AWE206
Area V
21 Feb 10
SP15
M
123/123
131/133
196/214
208/214
157/159
218/226
108/116
Mn211
Byron Bay
30 Jun 04
-
M
123/123
131/133
196/214
208/214
-/-
-/-
108/116
2010AWE207
Area V
21 Feb 10
SP94
M
123/127
131/133
192/198
214/214
153/163
203/210
106/108
Mn319
Hervey Bay
17 Sep 03
SP94
M
123/127
131/133
192/198
214/214
-/-
203/210
106/108
2010AWE210
Area V
22 Feb 10
SP94
F
123/123
133/139
198/208
208/220
165/165
199/214
106/112
Mn650
Hervey Bay
9 Sep 02
SP94
F
123/123
133/139
198/208
208/220
-/-
199/214
106/112
2010AWE213
Area V
27 Feb 10
SP102
F
123/127
131/131
194/196
206/212
155/163
199/230
104/108
Mn519
Byron Bay
2003
SP102
F
123/127
131/131
194/196
206/212
155/163
199/230
104/108
2010AWE215
Area V
28 Feb 10
SP1
M
123/123
133/143
196/216
212/214
161/163
218/238
106/106
Mno04NZ014
NewZealand
24 Jun 04
SP1
M
123/123
133/143
196/216
212/214
161/163
218/238
106/106
#loci
PI
8
4.63 X10-11
7
3.25 x10-9
6
2.3x10-7
7
1.34x10-9
7
7.7x10-11
8
7.4x10-13
10
4.33x10`14
151/151
109/115
149/151
196/200
149/151
113/115
151/151
198/206
151/151
109/115
153/157
198/206
153/157
115/115
143/153
200/204
143/153
111/115
137/151
200/204
137/151
115/115
115/115
151/153
151/153
196/198
196/198