Appendix 1. Supplemental Information
Methods
HMDS (hybrid multidimensional scaling) uses a matrix of dissimilarity values for the toxicity data
to create an ordination plot. This is done such that the rank order of dissimilarities of the samples is
reflected in their distances in ordination space relative to one another (Jongman et al., 1995). The extent
to which HMDS adequately represents the relationships is reflected in the stress value (Kruskal and Wish,
1978). The stress value defines the amount of scatter around the line of best fit through the HMDS
distances versus the actual distances (Clarke, 1993). The lower the stress value the better the
representation; generally stress values > 0.2 yield plots which can potentially be misleading or difficult to
interpret (Clarke, 1993).
The relationships between sediment toxicity and sediment contamination were examined with the
inclusion of the organic contaminant data. Test sites were ordinated again by HMDS, as a single group
without inclusion of Great Lakes reference data. Principal axis correlation and Monte Carlo permutation
tests were conducted as described in the text with the sediment organic contaminant data (PCBs, PAHs),
as well as sediment metal, nutrient, and particle size data. Initially, to examine general and dominant
patterns in the data, comparisons between the toxicity responses and contaminant conditions were made
based on integrative, compound variables (from either summation or multivariate ordination of
measurement variables). After this, to better detect less dominant (though significant) relationships
between two or a few variables, analyses were conducted using the original measurement variables (i.e.,
toxicity endpoints and concentrations of individual compounds). Concentrations of 10 metals (Cd, Cr,
Cu, Fe, Hg, Mg, Mn, Ni, Pb, Zn) and 3 nutrients (total Kjeldahl nitrogen, total organic carbon, total
phosphorus) were ordinated by principal components analysis (PCA). Data for all variables were ln(x)transformed. The eigenanalysis was performed on the correlation matrix. PAH data were integrated by
summing the concentrations of the individual compounds. The integrated descriptors of sediment toxicity
(axes scores from the HMDS) were plotted against the contaminant descriptors (PCA scores, total PCBs,
total PAHs (the latter two of which were ln(x)-transformed to improve linearity)). Relationships among
integrated (HMDS axes scores) and individual toxicity variables were also evaluated by plotting against
individual contaminant variables (ln(x)-transformed concentrations of 10 metals, 3 nutrients, PCBs and
16 PAHs in sediment). To determine whether toxicity was better explained by joint consideration of the
contaminant descriptors, a multiple linear regression involving the contaminant descriptors as predictors
was calculated for each toxicity descriptor as the response variable. The degree to which sediment
contaminants account for toxicity was assessed by fitting regression models using best subset procedures
(Draper and Smith, 1998). Available predictors were the above contaminant and nutrient variables, plus
mean sediment grain size. Models were fitted for (a) all combinations of metals and nutrients, (b) all
combinations of PCBs, PAHs and mean grain size, and then (c) all combinations of the best predictors
from the two groups. This procedure was used to avoid computational difficulties arising from working
with 32 predictors simultaneously. The best models were those having maximum explanatory power
(based on R2adjusted), minimum number of nonsignificant predictors, and minimum amount of predictor
multicollinearity.
Clarke, K.R., 1993. Non-parametric multivariate analyses of changes in community structure. Australian J. Ecol. 18: 117-143.
Draper, N.R., Smith, H., 1998. Applied regression analysis, 3rd Ed. John Wiley & Sons, Inc., New York
Jongman, R.H.G., Ter Braak, C.J.F., Van Tongeren, O.F.R., 1995. Data analysis in community and landscape ecology.
Cambridge University Press, UK. pp. 299.
Kruskal, J.B., Wish, M., 1978. Multidimensional scaling. Sage Publications, Beverley Hills California. pp. 93.
Results
4
RR04
RR03
2
7039
Axis 3
RR01
7038
0
7043
7061
7040
Hex surv
Hex gr
HyalRR05
gr
Hyal surv
RR02
-2
-4
-4
-2
0
Axis 1
2
4
Appendix1, Figure 1. Hybrid multidimensional scaling of subset of 2002 Randle Reef sites based on
Euclidean distance calculated from the mean of four bioassay endpoints, summarized on 2 of 3 axes.
Stress = 0.06. The 90% (inner), 99% (middle) and 99.9% (outer) probability ellipses are constructed from
105 Great Lakes reference sites whose individual scores are not shown. The directions of maximum
correlation of toxicity endpoints are shown as vectors.
Appendix 1, Table 1. Individual site prioritizations. Metal concentrations (mg kg-¹) exceeding the Severe
Effect Level and total PAHs greater than 100 mg kg-¹ are bolded.
1
Site
Total PAHs
Guideline1
RR09
RR22
RR55
RR04
RR07
RR10
RR11
RR12
RR13
RR30
RR31
RR32
RR36
RR59
RR72
RR74
RR75
RR43
RR47
RR56
RR57
RR58
RR60
RR64
RR06
RR37
7039
RR17
RR54
7043
7061
RR61
RR08
RR18
RR24
RR26
RR34
RR35
RR40
RR48
RR52
RR62
RR63
RR66
RR67
RR69
RR70
RR71
RR39
RR68
RR01
RR02
RR03
RR15
RR16
RR33
RR45
RR49
RR50
7038
RR14
RR25
7040
RR05
RR19
RR20
RR21
RR23
RR27
RR28
RR29
RR38
RR41
RR42
RR44
RR46
RR51
RR53
RR65
RR73
100
170.3
626.4
1047.1
128.6
135.8
208.8
45.7
34.4
1105
182.7
249.5
324.1
133.6
888.5
157.5
138.8
132.3
541.6
120.3
2474
1010.7
648.9
9048
237.7
46.4
98.0
14.5
53.4
20.9
73.9
24.6
122.5
332.2
254.8
111.8
247.8
134.6
166.8
171.6
213.8
372.5
120.0
612.2
704.0
289.6
281.2
487.9
230.8
40.6
67.7
5.0
12.5
4.7
22.0
9.9
11.3
2.2
24.1
36.6
8.0
25.1
9.8
7.5
6.2
5.8
10.8
2.6
8.2
5.6
1.0
4.4
9.2
5.2
7.5
50.4
20.8
18.8
2.1
48.4
63.5
Arsenic Cadmium Chromium Copper
33
<5
<5
5
7.5
10
30
31
22.9
<5
17
7.9
<5
12.2
<5
<5
8.5
<5
<5
<5
<5
<5
<5
7.6
9.0
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
5
5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
5
<5
<5
<5
<5
<5
<5
<5
<5
<5
<5
10
2.1
1.8
3.3
3.7
4.4
2.0
1.5
1.4
2.2
5.0
3.2
2.0
3.3
1.5
2.7
3.9
2.3
1.5
1.8
2.5
2.4
2.0
2.5
3.0
1.9
2.9
4.0
2.5
2.2
1.0
1.0
1.9
1.2
2.1
2.1
1.4
1.9
2.6
2.3
3.5
2.5
1.6
1.6
2.1
1.3
1.5
1.3
1.6
1.8
3.9
2.4
1.7
1.1
1.4
1.3
2.9
1.6
2.9
2.1
1.5
1.1
1.8
1.0
1.6
1.1
1.3
1.4
1.1
1.2
0.5
1.5
1.0
1.2
1.4
2.0
1.9
2.1
1.5
1.8
<1
110
80.8
53.2
92.3
104.4
82.4
90.0
142.4
111.5
67.0
57.8
94.3
77.2
104.9
56.4
73.9
98.6
72.1
80.2
43.3
87.8
67.3
72.8
82.2
88.0
87.6
81.0
71.7
46.6
82.7
48.8
90.7
59.6
58.9
78.0
82.3
76.4
54.8
72.4
59.6
143.5
82.1
77.3
109.8
73.6
65.3
55.7
72.2
63.6
42.9
84.7
43.2
98.0
38.9
32.8
53.4
61.4
23.2
86.4
73.8
55.9
51.1
48.9
68.6
76.8
48.0
29.1
21.6
56.7
41.8
30.4
48.2
45.8
35.1
20.3
52.8
38.0
68.9
39.7
65.8
37.3
110
68.6
39.0
80.0
59.8
98.9
131.1
705.6
608.5
46.6
75.7
55.0
28.7
68.2
33.2
58.0
66.9
49.5
36.7
38.9
44.6
59.0
48.7
62.3
29.1
76.1
68.9
67.0
101.1
61.9
25.2
56.3
35.4
33.8
55.8
58.6
43.8
37.4
61.4
52.6
69.6
46.8
38.1
34.3
43.6
35.8
38.5
41.2
37.6
48.4
71.3
47.4
44.3
31.2
70.3
58.5
48.9
16.6
49.5
65.0
41.4
62.7
64.9
31.5
47.4
30.5
46.1
18.2
35.4
31.5
21.5
39.7
37.1
29.3
28.5
38.1
32.4
57.3
17.7
30.7
26.1
Mercury
Nickel
Lead
Zinc
2
0.43
0.12
0.35
0.40
0.66
0.79
0.55
0.34
0.26
0.66
0.42
0.05
0.13
0.18
0.39
0.31
0.24
0.09
0.05
0.20
0.26
0.11
0.10
0.05
0.34
0.15
0.27
0.52
0.17
0.06
0.14
0.12
0.33
0.38
0.12
0.13
0.06
0.19
0.18
0.25
0.14
0.10
0.09
0.17
0.10
0.19
0.24
0.20
0.13
0.31
0.25
0.19
0.11
0.49
0.10
0.10
0.03
0.12
0.17
0.06
0.36
0.24
0.05
0.19
0.22
0.23
0.05
0.12
0.11
0.04
0.13
0.08
0.04
0.08
0.09
0.07
0.12
0.05
0.04
0.27
75
20.5
11.7
39.0
42.0
44.0
72.0
590.5
303.0
7.3
36.0
29.6
3.0
33.3
9.0
29.2
42.0
21.5
9.3
7.5
1.9
13.9
7.7
8.0
8.0
28.4
28.9
21.1
42.2
20.7
8.0
24.7
6.7
13.1
28.2
6.0
17.9
5.0
31.3
25.1
32.8
20.5
6.3
4.0
16.9
13.3
14.3
20.1
17.0
21.1
29.8
12.4
15.6
13.2
29.9
15.9
18.4
1.9
16.4
22.9
18.2
25.6
22.4
7.8
12.2
15.1
19.7
7.0
16.8
11.4
11.3
17.6
17.1
10.3
12.6
13.2
7.6
18.2
4.5
6.4
16.9
250
200.3
149.6
284.7
284.6
446.9
438.0
331.5
611.0
146.9
566.1
223.2
42.0
208.6
113.0
227.1
313.9
172.1
86.4
51.6
137.6
173.0
109.7
106.1
39.5
168.8
178.9
190.8
200.1
125.9
48.0
126.5
68.9
97.7
128.8
70.2
88.8
70.9
192.2
134.7
217.6
135.8
75.4
66.8
132.8
76.2
94.4
122.2
90.7
103.2
215.7
62.1
67.1
49.1
101.2
69.6
103.2
31.5
146.0
154.7
85.1
111.5
69.9
49.5
68.0
52.7
70.3
17.0
46.8
47.4
18.3
45.5
59.8
34.7
45.4
70.3
53.1
111.8
32.7
51.5
27.0
820
1158
726.7
1790
2160
2480
2350
1585
1560
575.7
2520
1838
186.0
1515
872.1
1765
2430
1164
430.6
259.5
586.4
979.8
652.2
477.0
182.0
900.9
1262
948.4
978.1
711.6
277.3
775.5
392.7
697.9
954.9
363.9
568.2
378.6
1499
1015
1710
1029
432.6
358.4
1058
494.1
677.5
986.7
604.7
698.5
1602
255.1
356.1
222.5
494.4
329.8
532.7
133.9
766.0
797.9
287.7
597.6
340.4
230.8
266.5
260.6
351.5
67.2
234.7
247.6
83.2
202.0
343.1
198.0
242.7
424.5
181.9
599.9
198.1
297.2
153.2
Toxicity
Band2
4
4
4
4
4
4
4
4
3
4
4
3
4
4
4
4
4
1
2
2
2
1
2
1
3
4
4
3
2
1
1
1
2
2
1
1
1
2
2
1
2
1
1
2
2
1
2
1
2
2
4
3
4
3
4
3
3
4
4
4
2
1
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
Outcome
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + high tox
high contam + high tox
high contam + high tox
high contam + high tox
low contam + low tox
low contam + low tox
low contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
high contam + low tox
low contam + low tox
high contam + low tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + high tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
low contam + low tox
Initial
Priority 3
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
4
4
4
4
non-priority
non-priority
non-priority
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
non-priority
3
4
4
4
4
4
4
4
4
4
4
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
100 mg kg-¹ for total PAHs and the Severe Effect Level for metals
Band 1=non-toxic, Band 2=potentially toxic, Band 3=toxic, Band 4=severely toxic
3
Based on 2002 chemistry and toxicity data only
4
Based on chemistry and toxicity and specific design elements (BBL et al., 2006)
2
Final
Priority 4
1
1
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
4
4
4
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority
non-priority