Supplementary Material

Article Title:

Broad-scale population genetic analysis of the New Zealand abalone, Haliotis iris

Journal Name:

Marine Biology

Authors:

Margaret Will1

Marie Hale1

David R. Schiel1

Neil J. Gemmell1, 2, 3

1 School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand

2 Centre for Reproduction and genomics, Department of Anatomy and Structural Biology, University of Otago, PO Box 913, Dunedin, New Zealand

3 Corresponding author, e-mail: , telephone: +64-3-479-6824, fax: +64-3-479-7254

SI Table 1: Polymorphism data for mitochondrial fragments for all samples (N=534).

Region / bp / Number of polymorphic sites / Number of haplotypes / Haplotype diversity
h S.D. / Nucleotide diversity
 S.D.
mtCOI / 459 / 33 / 42 / 0.53750.0250 / 0.00240.0017
ATPase8 – ATPase6 / 597 / 96 / 108 / 0.87570.0079 / 0.004800028
Concatenated / 1056 / 129 / 147 / 0.89950.0075 / 0.00370.0021

SI Table 2: Polymorphism Tajima’s D, and Fu’s Fs for concatenated mitochondrial fragments across sampling locations. Results were generated in Arlequin 3.5 (Excoffier et al. 2005). * indicates significance after Bonferroni correction (p = 0.0013, determined across SI Table 2 and Table 4).

Location / N / Number of polymorphic sites / Number of haplotypes
(number of private haplotypes) / Haplotype diversity
h S.D. / Nucleotide diversity
 S.D. / Tajima’s D
(p-value) / Fu’s Fs
(p-value)
AHU / 22 / 22 / 17 (7) / 0.9740.022 / 0.0040.002 / -1.165 (0.120) / -10.420 (<0.001)*
CBL / 12 / 11 / 5 (1) / 0.8490.059 / 0.0040.003 / 1.049 (0.875) / 1.910 (0.831)
CCB / 20 / 14 / 5 (0) / 0.8050.050 / 0.0040.002 / 0.436 (0.717) / 3.407 (0.930)
CHN / 20 / 15 / 10 (6) / 0.8740.052 / 0.0030.002 / -1.233 (0.101) / -3.015 (0.050)
CRW / 19 / 15 / 8 (2) / 0.8890.042 / 0.0040.002 / -0.478 (0.348) / -0.301 (0.456)
DBL / 15 / 21 / 12 (8) / 0.9620.040 / 0.0050.003 / -0.886 (0.198) / -4.726 (0.012)
DSD / 14 / 9 / 4 (0) / 0.5820.137 / 0.0020.002 / -0.544 (0.325) / 1.715 (0.822)
EAI / 24 / 19 / 10 (3) / 0.8770.038 / 0.0020.001 / -1.905 (0.014) / -3.005 (0.051)
GLN / 20 / 18 / 14 (5) / 0.9630.026 / 0.0030.002 / -1.233 (0.103) / -7.553 (<0.001)*
GOB / 19 / 12 / 7 (2) / 0.7840.074 / 0.0030.002 / -0.156 (0.488) / 0.163 (0.560)
IHM / 20 / 26 / 16 (9) / 0.9740.025 / 0.0060.003 / -0.754 (0.235) / -7.287 (0.003)
JCH / 20 / 17 / 7 (2) / 0.8470.042 / 0.0040.003 / -0.211 (0.460) / 1.301 (0.748)
MAT / 21 / 20 / 14 (6) / 0.9240.043 / 0.0030.002 / -1.459 (0.058) / -7.105 (0.001)*
MHP / 20 / 19 / 12 (5) / 0.9210.042 / 0.0030.002 / -1.639 (0.035) / -5.287 (0.004)
MTB / 22 / 7 / 8 (4) / 0.8180.052 / 0.0010.001 / -0.877 (0.206) / -3.313 (0.012)
NPT / 20 / 14 / 8 (2) / 0.8580.045 / 0.0040.002 / 0.162 (0.613) / 0.140 (0.549)
OCH / 13 / 12 / 6 (3) / 0.8210.082 / 0.0050.003 / 1.359 (0.929) / 1.370 (0.769)
OLB / 20 / 20 / 12 (7) / 0.9260.038 / 0.0050.003 / -0.295 (0.423) / -2.507 (0.132)
OPT / 19 / 23 / 13 (6) / 0.9300.047 / 0.0040.002 / -1.680 (0.030) / -5.886 (0.003)
PHD / 20 / 21 / 14 (8) / 0.9530.030 / 0.0050.003 / -0.521 (0.330) / -4.939 (0.016)
SPB / 21 / 29 / 18 (12) / 0.9810.023 / 0.0050.003 / -1.391 (0.066) / -11.431 (<0.001)*
STR / 15 / 15 / 6 (1) / 0.8190.064 / 0.0040.003 / 0.063 (0.566) / 1.545 (0.778)
TCL / 20 / 20 / 13 (4) / 0.9110.054 / 0.0040.002 / -1.306 (0.085) / -5.424 (0.006)
TIM / 23 / 14 / 10 (5) / 0.8540.049 / 0.0020.001 / -1.739 (0.022) / -4.212 (0.006)
TSK / 20 / 14 / 8 (3) / 0.8470.051 / 0.0030.002 / -1.171 (0.118) / -1.207 (0.254)
WAI / 20 / 23 / 12 (4) / 0.9370.033 / 0.0050.003 / -1.011 (0.159) / -2.869 (0.087)
WLG / 20 / 31 / 16 (9) / 0.9630.033 / 0.0040.003 / -1.846 (0.018) / -8.951 (<0.001)*
WST / 15 / 10 / 5 (0) / 0.7810.074 / 0.0030.002 / -0.412 (0.382) / 1.031 (0.726)

SI Fig.1: Delaunay triangulation and Voronoï tessellation for analysis with Monmonier’s (1973) maximum difference algorithm implemented in Barrier 2.2 (Manni et al. 2004). Green lines are the Delaunay triangulation. Blue polygons are the Voronoï tessellation. Small blue dots are virtual points. Outside virtual points were used to close the tessellation. A) Full triangulation and tessellation B) Modified triangulation and tessellation to reflect New Zealand’s coastline as best as possible. C) Location ID number and sample abbreviation.

AB

ID number / Abbreviation / ID number / Abbreviation
1 / AHU / 15 / MTB
2 / CBL / 16 / NPT
3 / CCB / 17 / OCH
4 / CHN / 18 / OLB
5 / CRW / 19 / OPT
6 / DBL / 20 / PHD
7 / DSD / 21 / SPB
8 / EAI / 22 / STR
9 / GLN / 23 / TCL
10 / GOB / 24 / TIM
11 / IHM / 25 / TSK
12 / JCH / 26 / WAI
13 / MAT / 27 / WLG
14 / MHP / 28 / WST

C
SI Fig. 2: Genetic differentiation in New Zealand abalone. A) Genetic differences among 28 locations (see SI Fig. 1c) were summarized in a single pairwise ST matrix that was used to compute the first five barriers (yellow) with Monmonier’s (1973) maximum difference algorithm implemented in Barrier 2.2 (Manni et al. 2004). The first five barriers were also analyzed on 100 resampled matrices. The thickness of each edge (red) is proportional to the number of times it was included in one of the 500 computed barriers. B–F) First–fifth rank barriers (red) based on 100 resampled matrices. G) Similar to A, but genetic differences among locations were summarized with the net number of nucleotide differences between populations (DA; Nei and Li 1979).

A. Analysis based on pairwise ST

B. First rank barrierC. Second rank barrier


D. Third rank barrierE. Fourth rank barrier

F. Fifth rank barrierG Analysis based on DA

Table 3: Values of , sum of squared deviation (SSD), and raggedness index (Harpending et al. 1993) estimated from the demographic expansion model (Schneider and Excoffier 1999). Results were generated in Arlequin 3.5 (Excoffier et al. 2005).

Sample /  / SSD (p-value) / Raggedness index (p-value)
AHU / 2.0 / 0.003 (0.767) / 0.022 (0.660)
CBL / 9.8 / 0.056 (0.331) / 0.061 (0.705)
CCB / 9.8 / 0.082 (0.131) / 0.087 (0.356)
CHN / 1.7 / 0.019 (0.159) / 0.076 (0.400)
CRW / 0.5 / 0.288 (0.005) / 0.046 (0.997)
DBL / 6.7 / 0.014 (0.483) / 0.025 (0.786)
DSD / 0.3 / 0.060 (0.149) / 0.148 (0.625)
EAI / 1.9 / 0.004 (0.579) / 0.050 (0.568)
GLN / 3.6 / 0.005 (0.456) / 0.039 (0.389)
GOB / 9.2 / 0.070 (0.297) / 0.100 (0.510)
IHM / 7.8 / 0.011 (0.660) / 0.015 (0.891)
JCH / 9.8 / 0.043 (0.321) / 0.041 (0.718)
MAT / 1.2 / 0.109 (0.020) / 0.017 (0.999)
MHP / 1.6 / 0.048 (0.036) / 0.035 (0.865)
MTB / 1.5 / 0.008 (0.389) / 0.095 (0.268)
NPT / 9.9 / 0.031 (0.488) / 0.044 (0.749)
OCH / 9.9 / 0.047 (0.269) / 0.058 (0.611)
OLB / 4.0 / 0.011 (0.599) / 0.022 (0.809)
OPT / 1.5 / 0.089 (0.015) / 0.035 (0.888)
PHD / 0.8 / 0.026 (0.392) / 0.030 (0.643)
SPB / 1.7 / 0.006 (0.713) / 0.015 (0.842)
STR / 9.5 / 0.063 (0.194) / 0.059 (0.587)
TCL / 8.0 / 0.017 (0.686) / 0.026 (0.915)
TIM / 1.5 / 0.021 (0.130) / 0.133 (0.102)
TSK / 1.6 / 0.018 (0.190) / 0.062 (0.549)
WAI / 0.8 / 0.259 (0.004) / 0.016 (1.000)
WLG / 1.6 / 0.129 (0.013) / 0.012 (0.999)
WST / 0.6 / 0.136 (0.025) / 0.069 (0.886)

Table 4: Values of , sum of squared deviation (SSD), and raggedness index (Harpending et al. 1993) estimated from the spatial expansion model (Ray et al. 2003, Excoffier et al. 2004). Results were generated in Arlequin 3.5 (Excoffier et al. 2005).

Sample /  / SSD (p-value) / Raggedness index (p-value)
AHU / 2.02 / 0.003 (0.733) / 0.022 (0.660)
CBL / 7.30 / 0.046 (0.358) / 0.061 (0.705)
CCB / 7.70 / 0.059 (0.154) / 0.087 (0.356)
CHN / 1.67 / 0.019 (0.106) / 0.076 (0.400)
CRW / 0.50 / 0.022 (0.385) / 0.046 (0.997)
DBL / 5.65 / 0.020 (0.311) / 0.025 (0.786)
DSD / 8.07 / 0.047 (0.324) / 0.148 (0.625)
EAI / 1.91 / 0.004 (0.474) / 0.050 (0.568)
GLN / 3.57 / 0.005 (0.426) / 0.039 (0.389)
GOB / 7.34 / 0.059 (0.186) / 0.100 (0.510)
IHM / 2.29 / 0.017 (0.226) / 0.015 (0.891)
JCH / 7.16 / 0.037 (0.333) / 0.041 (0.718)
MAT / 1.23 / 0.001 (0.944) / 0.017 (0.999)
MHP / 1.54 / 0.004 (0.640) / 0.035 (0.865)
MTB / 1.52 / 0.008 (0.295) / 0.095 (0.268)
NPT / 0.20 / 0.033 (0.218) / 0.044 (0.749)
OCH / 7.51 / 0.034 (0.495) / 0.058 (0.611)
OLB / 2.53 / 0.011 (0.563) / 0.022 (0.809)
OPT / 1.55 / 0.007 (0.590) / 0.035 (0.888)
PHD / 0.78 / 0.026 (0.213) / 0.030 (0.643)
SPB / 1.68 / 0.006 (0.678) / 0.015 (0.842)
STR / 7.21 / 0.047 (0.323) / 0.059 (0.587)
TCL / 0.70 / 0.012 (0.525) / 0.026 (0.915)
TIM / 1.53 / 0.021 (0.072) / 0.133 (0.102)
TSK / 1.05 / 0.018 (0.164) / 0.062 (0.549)
WAI / 0.76 / 0.013 (0.489) / 0.016 (1.000)
WLG / 1.56 / 0.006 (0.728) / 0.012 (0.999)
WST / 0.59 / 0.031 (0.172) / 0.069 (0.886)