Figure A1 Mean pairwise genetic relatedness (LR) within NZ sea lion colonies. Error bars represent standard error.

Figure A2 Isolation by distance results (genetic distance, FST, by geographic distance, km). R2=0.0227

Figure A3 Mean Ln probability of data (±SE, squares) based on 10 independent replicates for each value of K in Structure (Pritchard et al. 2000), and ΔK (circles) calculated in Structure Harvester (Earl & von Holdt 2012).

Table A1 Mitochondrial DNA primer sequences used in PCR amplification and DNA sequencing of PCR products.

Primer name / Primer sequence 5’ to 3’
NZSL cyt b L / ATTCCCACATGGAATTTAACCA
NZSL cyt b H / TGCCTCTTCCTTGAGTCTTCTTAGG
L-NZSL dloop-tRNApro1 / CTCAAGGAAGAGGCAACAGC
H-NZSL dloop-tRNAphe1 / GAAGGGCTAGGACCAAACCT
NZSL dloop H3 / TGTTTGTGTTTTGTGACCTG

1 Collins et al. 2014

Table A2 Oligonucleotide sequences, multiplex number and dye label of microsatellite loci used.

Locus / Oligonucleotide sequence (5’-3’)
(forward and reverse) / Multiplex No. / Dye Label
PvcA1 / GAGTATACCTCCATACTACAC
AGTTGTTCTCCTGACCCAAG / 1 / FAM
G1A2 / GACCCTGCATACTCTCCTCTGATG
GCACTGTCCTTGCGTAGAAGTGAC / 1 / FAM
ZcwE033 / CTACACCTTTGGCTCCTCACTCT
AGAACTAAGGAGCCTGTCTCGTGG / 1 / FAM
Hg8.104 / TAGTGTTTGGAAATGAGTTGGCA
ACTTGATCCTTGTGAATCCCAGC / 1 / NED
OrrFcB75 / GAACCAGGGAGGAAGACAGAGTG
CAGACTGTATCAGGAGGCTTTGG / 1 / NED
Hg6.14 / TGCACCAGAGCCTAAGCAGACTG
CCACCAGCCAGTTCACCCAG / 1 / VIC
Hg6.34 / CAGGGGACCTGAGTGCTTATG
GACCCAGCATCAGAACTCAAG / 1 / VIC
Lc286 / TCATATAATACCCACCTCTGTAAG
GACCCAGCATCAGAACTCAAG / 1 / PET
Pv97 / TAGTGTTTGGAAATGAGTTGGCA
ACTGATCCTTGTGAATCCCAGC / 1 / PET
HI166 / CACTTATCTCGCCCTATATCCA
CAGCCAGCCAGTTCACCCAG / 2 / FAM
OrrFCB15 / CTATAACTGGATAGATGATGGTGAC
CCCAAGCATAAGGTATCTTGGCC / 2 / FAM
Lc56 / ATCTTCAGGCTTTCTTCT
TTCACGGACTCAAATAAT / 2 / VIC
ZcCgDh1.88 / gcactacttattcagtagca
CCCCACTGTGTTCATTCAAC / 2 / VIC
ZcCgDh3.68 / AATCACACATCCTTACTCTC
GCCATAAAATTCTAGGTTG / 2 / NED
Hg4.24 / AATCGAAATGCTGAGCCTCC
TGATTTGACTTCCCTTCCCTG / 2 / NED
ZcCgDh5.168 / TGCTCAGTCACCCTTCTTG
CAGAAACGTGGAATACACAG / 2 / PET

1Coltman et al. 1996; 2PaetkauStrobeck 1994; 3 Wolf et al. 2005; Allen at al. 1995; 5 Buchanan et al. 1998; 6 Davis et al. 2002; 7 Goodman 1997; 8 Hernandez-Velazquez et al. 2005

Table A3 Population pairwise FST values for D-Loop (below diagonal) and cyt b (above diagonal) sequence data – distance method: pairwise differences. Asterisk indicates significant with a P-value less than 0.05, values in bold are significant following Bonferroni correction. DI=Dundas Island, FE=Figure of Eight Island, OP=Otago Peninsula, Sandy Bay=SB, Stewart Island=SI, Davis Point=DP, Paradise Point=PP.

DI / FE / OP / SB / SI / DP / PP
DI / 0.31673 / -0.03704 / 0.40563* / -0.03294 / 0.00000* / 0.00000*
FE / 0.00000* / 0.04654* / 0.02528 / 0.29704* / 0.42515* / 0.52310*
OP / 0.01786 / 0.01786* / 0.38096 / -0.02517 / 0.05285 / 0.04762*
SB / -0.01587 / 0.00000* / 0.01786* / 0.00000* / 0.47858* / 0.54130*
SI / 0.01786 / 0.00227* / 0.00461* / 0.01786 / 0.04681 / 0.03709
DP / -0.01587 / -0.01587* / 0.01786* / -0.01587 / 0.00227 / 0.00000*
PP / 0.00000* / 0.00000* / 0.01786 / 0.00000* / 0.00227 / 0.00000*

Table A4 Allelic richness (A) based on the minimum sample size, number of successfully genotyped individuals per locus (n), polymorphism characteristics of microsatellite loci including departure from Hardy-Weinberg equilibrium and null allele frequency. *P-value indicates significance of deviation between HO and HE.

Locus / A / n / Allele size range / HO / HE / P-value* / HWE / Null allele frequency
PvcA / 5.12 / 248 / 167-181 / 0.664 / 0.692 / 0.0263 / 0.970 / 0.067
G1A / 3.58 / 246 / 197-205 / 0.636 / 0.590 / 0.0001 / 0.849 / 0.046
ZcwE03 / 3.04 / 261 / 226-230 / 0.454 / 0.455 / 0.4289 / 0.416 / 0.027
Hg8.10 / 3.04 / 260 / 202-206 / 0.410 / 0.451 / 0.1963 / 0.987 / 0.023
OrrFcB7 / 5.72 / 262 / 216-226 / 0.730 / 0.765 / 0.1199 / 0.937 / 0.016
Hg6.1 / 5.30 / 252 / 166-184 / 0.597 / 0.616 / 0.8776 / 0.568 / 0.008
Hg6.3 / 5.60 / 265 / 244-264 / 0.711 / 0.723 / 0.0089 / 0.700 / 0.007
Lc28 / 3.84 / 255 / 159-165 / 0.559 / 0.643 / 0.0000 / 0.999 / 0.164
Pv9 / 3.29 / 255 / 192-202 / 0.490 / 0.517 / 0.1974 / 0.989 / 0.031
HI16 / 4.67 / 265 / 166-182 / 0.781 / 0.709 / 0.1801 / 0.002 / 0.000
OrrFCB1 / 6.63 / 261 / 198-226 / 0.668 / 0.706 / 0.0074 / 1.000 / 0.114
Lc5 / 3.70 / 263 / 172-180 / 0.427 / 0.455 / 0.1794 / 0.976 / 0.024
ZcCgDh1.8 / 1 / 262 / 202 / 0.000 / 0.000 / 0.0001 / 1.000 / 0.049
ZcCgDh3.6 / 3.98 / 266 / 244-252 / 0.655 / 0.682 / 0.8399 / 0.916 / 0.018
Hg4.2 / 7.52 / 256 / 170-184 / 0.764 / 0.842 / 0.0089 / 0.999 / 0.055
ZcCgDh5.16 / 7.29 / 266 / 228-260 / 0.829 / 0.826 / 0.4183 / 0.730 / 0.028

Table A5 Mean polymorphism characteristics across all 14 loci for P. hookeri colonies

Colony / n / Mean no. alleles / HO / HE
Dundas Island / 49 / 5.867 / 0.686 / 0.683
Figure of Eight Island / 14 / 4.400 / 0.631 / 0.599
Paradise Point / 54 / 5.993 / 0.623 / 0.634
Davis Point / 54 / 6.000 / 0.621 / 0.650
Otago Peninsula / 48 / 5.600 / 0.622 / 0.634
Sandy Bay / 36 / 6.200 / 0.622 / 0.639
Stewart Island / 16 / 4.400 / 0.558 / 0.585

Table A6 Pairwise FST values for microsatellite data (all loci) for all populations. Asterisks indicate FST values with a significant P value (P ≤ 0.05), no values were significant following Bonferroni correction.

DI / FE / PP / DP / OP / SB / SE
DI / -
FE / 0.0040 / -
PP / 0.0047* / 0.0178* / -
DP / 0.0097 / 0.0229* / -0.0017* / -
OP / 0.0297* / 0.0582* / 0.0366* / 0.0440* / -
SB / 0.0032* / 0.0176* / 0.0065* / 0.0122* / 0.0320 / -
SE / 0.0348* / 0.0403* / 0.0542* / 0.0597* / 0.0874* / 0.0471* / -

Table A7Estimates of migration rates (m, proportion of individuals) among breeding colonies of NZ sea lions generated using BayesAss 3.0.

The means of the posterior distributions of the migration rate into each population is shown, with the standard deviation in brackets. The populations from which each individual was sampled from are listed in the rowsand columns represent the populations from which they migrated. Values along the diagonal are the proportions of individuals within a population derived from that population.

Sample location / Putative population of origin
DI / FE / PP / DP / OP / SB / SI
DI / 0.67 (0.01) / 0.01 (0.01) / 0.01 (0.01) / 0.27 (0.02) / 0.01 (0.01) / 0.03 (0.02) / 0.01 (0.01)
FE / 0.05 (0.03) / 0.68 (0.02) / 0.02 (0.02) / 0.18 (0.04) / 0.02 (0.02) / 0.03 (0.02) / 0.02 (0.02)
PP / 0.01 (0.01) / 0.01 (0.01) / 0.67 (0.01) / 0.29 (0.02) / 0.01 (0.01) / 0.01 (0.01) / 0.01 (0.01)
DP / 0.02 (0.02) / 0.01 (0.01) / 0.01 (0.01) / 0.94 (0.02) / 0.01 (0.01) / 0.01 (0.01) / 0.01 (0.01)
OP / 0.02 (0.01) / 0.01 (0.01) / 0.01 (0.01) / 0.12 (0.05) / 0.82 (0.05) / 0.02 (0.01) / 0.01 (0.01)
SB / 0.03 (0.03) / 0.01 (0.01) / 0.01 (0.01) / 0.25 (0.04) / 0.02 (0.01) / 0.68 (0.01) / 0.01 (0.01)
SI / 0.21 (0.04) / 0.01 (0.01) / 0.01 (0.01) / 0.04 (0.03) / 0.02 (0.02) / 0.02 (0.02) / 0.68 (0.02)