Online Resources for:

Conservation Genetics

Historic DNA reveals contemporary population structure results from anthropogenic effects, not pre-fragmentation patterns

LISA N. TRACY, IAN G. JAMIESON

Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand

Correspondence: Ian G. Jamieson. Email: ,

Online Resource 1: Location, date, and accession numbers for museum samples

Accession Number / Contributor / Location / Date
AV4560 / OtagoMuseum, NZ / Dunedin / 1873
AV555 / OtagoMuseum, NZ / Stewart Island / pre-1962
AV1000 / CanterburyMuseum, NZ / Owen Junction / 1932
AV552 / OtagoMuseum, NZ / Stewart Island / pre-1962
AV553 / OtagoMuseum, NZ / Otago / c. 1890
AV999 / CanterburyMuseum, NZ / Kaituna, Richmond / 1891
AV1001 / CanterburyMuseum, NZ / Tophouse / 1933
AV2638 / CanterburyMuseum, NZ / Owen Junction / 1928
AV2639 / CanterburyMuseum, NZ / Akaroa / 1910
AV2251 / CanterburyMuseum, NZ / Dunedin / 1885
AV2640 / CanterburyMuseum, NZ / Takaka / 1915
AV1004 / CanterburyMuseum, NZ / Tophouse / 1933
AV1005 / CanterburyMuseum, NZ / Owen Junction / 1929
AV1006 / CanterburyMuseum, NZ / Owen Junction / 1932
AV2252 / CanterburyMuseum, NZ / Dunedin / 1911
AV12569 / CanterburyMuseum, NZ / Cape Farewell / 1891
LB4863 / AucklandMuseum, NZ / Tophouse / 1933
LB4864 / AucklandMuseum, NZ / Dunedin / 1892
LB4858 / AucklandMuseum, NZ / Otago / c. 1892
LB4852 / AucklandMuseum, NZ / Nelson / c. 1856
LB4856 / AucklandMuseum, NZ / Otago / c. 1892
LB4860 / AucklandMuseum, NZ / Owen Junction / 1932
LB4861 / AucklandMuseum, NZ / Owen Junction / 1932
LB4862 / AucklandMuseum, NZ / Tophouse / 1933
JHF5290; W7564 / RoyalOntarioMuseum / Dunedin / pre-1904
JHF5291; W7567 / RoyalOntarioMuseum / Dunedin / pre-1904
JHF14917 / RoyalOntarioMuseum / Dunedin / 1885
JHF17111 / RoyalOntarioMuseum / Dunedin / c. 1880
1897.12.6.3 / The NaturalHistoryMuseum (UK) / Milford Sound / pre-1897
1902.2.21.31 / The NaturalHistoryMuseum (UK) / Dusky Sound / 1901
1902.2.21.32 / The NaturalHistoryMuseum (UK) / Dusky Sound / 1901
1903.7.17.9 / The NaturalHistoryMuseum (UK) / Dusky Sound / 1901
1926.10.10.36 / The NaturalHistoryMuseum (UK) / Taramakau / 1876
1926.10.10.37 / The NaturalHistoryMuseum (UK) / Taramakau / 1876
1927.12.18.307 / The NaturalHistoryMuseum (UK) / Preservation Inlet / 1889
1927.12.18.308 / The NaturalHistoryMuseum (UK) / Preservation Inlet / 1889
1969.52.1068 / The NaturalHistoryMuseum (UK) / Christchurch / 1892
683537 / AmericanMuseum of Natural History / Dunedin / 1874
683538 / AmericanMuseum of Natural History / Dunedin / 1874
683539 / AmericanMuseum of Natural History / Dunedin / pre-1930
JHF 31429 / RoyalOntarioMuseum / Canterbury Plains / 1875
27/Syl/52/b/5 / UniversityMuseum of Zoology Cambridge / Milford Sound / 1898
27/Syl/52/b/6 / UniversityMuseum of Zoology Cambridge / Milford Sound / 1898
66291 / Smithsonian Institution / Bealey / 1872
66290 / Smithsonian Institution / Bealey / 1872
109195 / Smithsonian Institution / Otago / pre-1886
O.37421 / AustralianMuseum / Doubtful River / 1938
O.37422 / AustralianMuseum / Doubtful River / 1938
O.37423 / AustralianMuseum / LewisPass / 1939
O.37424 / AustralianMuseum / LewisPass / 1939
A.499 / AustralianMuseum / Dunedin / pre-1887
A.501 / AustralianMuseum / Dunedin / pre-1887
A.502 / AustralianMuseum / Dunedin / pre-1887
NMW 51.403 / ViennaNaturalHistoryMuseum / Dusky Sound / 1884
NMW 12.484 / ViennaNaturalHistoryMuseum / Dusky Sound / 1884
NMW 62.485 / ViennaNaturalHistoryMuseum / Dusky Sound / 1884
NMW 12.486 / ViennaNaturalHistoryMuseum / Paringa / 1887
NMW 51.404 / ViennaNaturalHistoryMuseum / Paringa / 1887
NMW 12.488 / ViennaNaturalHistoryMuseum / Paringa / 1887
NMW 12.487 / ViennaNaturalHistoryMuseum / Paringa / 1887

Online Resource 2.Optimized PCR conditions used to amplify mohua microsatellite loci.

Locus / Species / Reference / Primer Sequence (5’-3’) / Allele Size
(bp) / Anneal (°C) / Cycles
at Ta / Betaine/
DMSO
Apco29 / Florida scrub jay Aphelocoma coerulescens / Stenzler and
Fitzpatrick 2002 / f GGGTTCCAAGACAAAATCATAGTG
r CATCTGGAACTGGCATTTGCTTA / 86-95 / 45 / 35 / No
Fhu2 / Pied flycatcher Ficedula hypoleuca / Primmer et al. 1996 / f GTGTTCTTAAAACATGCCTGGAGG
r GCACAGGTAAATATTTGCTGGGCC / 129-147 / 45 / 35 / Yes
LEI160 / Chicken Gallus gallus / Crooijmans et al. 1997 / f CAAAGTAATCAGCTTGTGCTAC r CATTTCCACCGCATTGAGCAG / 101-107 / 45 / 35 / No
Hru2 / Barn Swallow Hirundo rustica / Primmer et al. 1995 / f CATCCAGAGAGGGATGGAAAGAGG
r GAAAAGATTATTTTTCTTTCTCCC / 133-139 / 45 / 40 / No
Hru7 / Barn Swallow Hirundo rustica / Primmer et al. 1995 / f GCATTCACAGTGTAGACAATG
r GATCACTATGAGTCCCTGGAA / 83-89 / 45 / 35 / No
Mcyu4 / Superb fairywren Malunus cyaneus / Double et al. 1997 / f ATAAGATGACTAAGGTCTCTGGTG
r TAGCAATTGTCTATCATGGTTTG / 126-130 / 45 / 35 / No
Pau18 / South Island robin Petroica australis / T. King pers. comm. / f AAAGCATGGATGCAATCC
r GGCAGTTTAAGCCTCATG / 119-122 / 45 / 35 / No
Pcc6 / South Island saddleback Philesturnus carunculatus
carunculatus / T. King pers. comm. / f GCCAGGTATCCACTGAGG
r ACCCCAAATTATGGACAC / 158-164 / 45 / 35 / Yes
Pcc26 / South Island saddleback Philesturnus carunculatus carunculatus / T. King pers. comm. / f ACTGTTTCCTACCCACTG
r TTCTGTAATTTACCATGC / 110-116 / 45 / 35 / No
Pcc38 / South Island saddleback Philesturnus carunculatus carunculatus / T. King pers. comm. / f ATATCAATGCTGCTCTAG
r GCAGATTTAGGAATCCAC / 101-103 / 45 / 30 / No
4H2 / NorthIsland saddleback
Philesturnus carunculatus rustafer / T. King pers. comm. / f GTTTTGACCTACAGAGAGAG
r GATAGGACAATCAACAGGCT / 109-111 / 60 / 35 / Yes

Online Resource 3a. Pairwise FST values between contemporary populations presented in the top semi-matrix, with corresponding P-values in the lower semi-matrix.

Catlins
(19) / Blue Mtns
(17) / Rowallan
(14) / Murchison
Mtns. (20) / Dart
(54) / Lands
(21)
Catlins (19) / – / 0.026 / 0.117 / 0.108 / 0.085 / 0.310
BlueMtns(17) / 0.028 / – / 0.070 / 0.061 / 0.041 / 0.238
Rowallan (14) / <0.001 / 0.004 / – / 0.042 / 0.010 / 0.114
Murchison (20) / <0.001 / <0.001 / 0.005 / – / 0.024 / 0.128
Dart (54) / <0.001 / 0.031 / 0.111 / 0.006 / – / 0.096
Lands (21) / <0.001 / <0.001 / <0.001 / <0.001 / 0.003 / –

Online Resource 3b.Pairwise FST values between historic regions presented in the top semi-matrix, with corresponding P-values in the lower semi-matrix.

Otago
(17) / Fiordland
(10) / Canterbury
(7) / Nelson
(14)
Otago (17) / – / 0.045 / 0.081 / 0.126
Fiordland (10) / 0.060 / – / 0.025 / 0.034
Canterbury (7) / 0.063 / 0.193 / – / -0.027
Nelson (14) / <0.001 / 0.065 / 0.891 / –

Online Resource4: Allele frequencies for all loci separated by population.Historicregions are indicated as Nels= Nelson, Cant=Canterbury, Otag=Otago and Fiord=Fiordland.Contemporary populations are indicated as Land=Landsborough, Dart=Dart, Murc=MurchisonMountains, Rowa=Rowallan, Blue=Blue Mountains, Catl=Catlins.

Locus / Allele / Historic / Contemporary
Size / Nels / Cant / Otag / Fiord / Land / Dart / Murc / Rowa / Blue / Catl
Fhu2 / 123 / 0.346 / 0.250 / 0.033 / 0.150 / 0.500 / 0.213 / 0.325 / 0.286 / 0.000 / 0.000
127 / 0.000 / 0.125 / 0.100 / 0.050 / 0.214 / 0.046 / 0.000 / 0.036 / 0.053 / 0.029
129 / 0.231 / 0.125 / 0.000 / 0.050 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
133 / 0.000 / 0.125 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.036 / 0.000 / 0.000
139 / 0.000 / 0.000 / 0.033 / 0.200 / 0.119 / 0.176 / 0.000 / 0.071 / 0.079 / 0.000
141 / 0.269 / 0.125 / 0.767 / 0.450 / 0.143 / 0.491 / 0.575 / 0.571 / 0.711 / 0.882
143 / 0.039 / 0.250 / 0.033 / 0.100 / 0.024 / 0.074 / 0.100 / 0.000 / 0.158 / 0.088
145 / 0.039 / 0.000 / 0.033 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
147 / 0.077 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Hru2 / 131 / 0.077 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
133 / 0.000 / 0.000 / 0.000 / 0.050 / 0.125 / 0.139 / 0.200 / 0.036 / 0.026 / 0.177
135 / 0.115 / 0.125 / 0.500 / 0.300 / 0.125 / 0.222 / 0.450 / 0.321 / 0.500 / 0.324
137 / 0.692 / 0.750 / 0.450 / 0.650 / 0.750 / 0.546 / 0.325 / 0.643 / 0.421 / 0.441
139 / 0.077 / 0.125 / 0.050 / 0.000 / 0.000 / 0.093 / 0.025 / 0.000 / 0.053 / 0.059
141 / 0.039 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Apco29 / 86 / 0.643 / 0.714 / 0.500 / 0.500 / 0.905 / 0.722 / 0.900 / 0.750 / 0.605 / 0.559
89 / 0.107 / 0.000 / 0.206 / 0.150 / 0.000 / 0.222 / 0.100 / 0.071 / 0.395 / 0.324
92 / 0.214 / 0.143 / 0.029 / 0.150 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
95 / 0.036 / 0.143 / 0.265 / 0.200 / 0.095 / 0.056 / 0.000 / 0.179 / 0.000 / 0.118
Pcc26 / 110 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.074 / 0.000 / 0.179 / 0.053 / 0.000
112 / 0.077 / 0.000 / 0.031 / 0.100 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
114 / 0.577 / 0.700 / 0.969 / 0.900 / 1.000 / 0.926 / 1.000 / 0.821 / 0.921 / 1.000
116 / 0.346 / 0.300 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.026 / 0.000
Hru7 / 83 / 0.125 / 0.083 / 0.219 / 0.300 / 0.476 / 0.389 / 0.200 / 0.429 / 0.237 / 0.147
87 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.026 / 0.000
88 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
89 / 0.875 / 0.917 / 0.781 / 0.700 / 0.524 / 0.611 / 0.800 / 0.571 / 0.737 / 0.853
LEI160 / 101 / 0.955 / 1.000 / 0.917 / 1.000 / 0.619 / 0.880 / 0.875 / 1.000 / 0.842 / 1.000
105 / 0.000 / 0.000 / 0.042 / 0.000 / 0.381 / 0.120 / 0.125 / 0.000 / 0.132 / 0.000
107 / 0.046 / 0.000 / 0.042 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.026 / 0.000
Pau18 / 119 / 0.833 / 1.000 / 0.955 / 0.650 / 0.929 / 0.889 / 0.925 / 0.893 / 0.790 / 0.941
121 / 0.167 / 0.000 / 0.000 / 0.350 / 0.071 / 0.083 / 0.075 / 0.107 / 0.211 / 0.059
122 / 0.000 / 0.000 / 0.046 / 0.000 / 0.000 / 0.028 / 0.000 / 0.000 / 0.000 / 0.000
Mcyu4 / 126 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.009 / 0.000 / 0.000 / 0.000 / 0.000
128 / 0.393 / 0.417 / 0.500 / 0.500 / 0.833 / 0.556 / 0.575 / 0.571 / 0.342 / 0.235
130 / 0.607 / 0.583 / 0.500 / 0.500 / 0.167 / 0.435 / 0.425 / 0.429 / 0.658 / 0.765
Pcc6 / 158 / 0.923 / 0.800 / 0.625 / 0.950 / 0.976 / 0.759 / 0.825 / 0.964 / 0.737 / 0.677
162 / 0.077 / 0.200 / 0.375 / 0.050 / 0.024 / 0.241 / 0.175 / 0.036 / 0.263 / 0.118
164 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.206
4H2 / 109 / 0.958 / 1.000 / 0.929 / 0.900 / 1.000 / 0.982 / 1.000 / 1.000 / 0.974 / 0.794
111 / 0.000 / 0.000 / 0.071 / 0.100 / 0.000 / 0.019 / 0.000 / 0.000 / 0.026 / 0.206
113 / 0.042 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Pcc38 / 101 / 0.750 / 0.917 / 0.964 / 0.850 / 0.476 / 0.759 / 0.675 / 0.786 / 0.921 / 0.941
103 / 0.250 / 0.083 / 0.036 / 0.150 / 0.524 / 0.241 / 0.325 / 0.214 / 0.079 / 0.059