Detailed statistical results - PLOS

Supplement to 'Effects of cnidarian biofouling on salmon gill health and development of Amoebic gill disease'

Detailed statistical results Significant terms are marked in red

Non-specific gill score AVERAGE Non-specific gill score Exposure day + 1 dphe PERMANOVA table of results Source Treatment Time Treatment x Time Residuals Total

df 1 1 1 28 31

SS 1.5313 0.28125 0.78125 7.375 9.9688

MS 1.5313 0.28125 0.78125 0.26339

Pseudo-F 5.8136 1.0678 2.9661

P(perm) 0.0245 0.3216 0.098

df 3 5 4 15 20 192 239

SS 0.083333 1.65 0.83333 5.3167 5.9667 44 57.85

MS 0.027778 0.33 0.20833 0.35444 0.29833 0.22917

Pseudo-F 0.13333 1.1061 0.90909 1.1881 1.3018

P(perm)

df 3 5 4 15 212 239

SS 0.083333 1.65 0.83333 5.3167 49.967 57.85

MS 0.027778 0.33 0.20833 0.35444 0.23569

Pseudo-F 0.13333 1.4001 0.88392 1.5038

P(perm)

3 dphe onwards PERMANOVA table of results Source Treatment Time Tank (Treatment) Treatment x Time Tank (Treatment) x Time Residuals Total

0.3912 0.4734 0.3498 0.1726

P(MC) 0.9409

Pooled terms Tank (Treatment) x Time PERMANOVA table of results Source Treatment Time Tank (Treatment) Treatment x Time Pooled Total

0.2168 0.4814 0.1068

P(MC) 0.9382

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Pooled terms Tank (Treatment) Tank (Treatment) x Time PERMANOVA table of results Source Treatment Time Treatment x Time Pooled Total

df 3 5 15 216 239

SS 0.083333 1.65 5.3167 50.8 57.85

MS 0.027778 0.33 0.35444 0.23519

Pseudo-F 0.11811 1.4031 1.5071

P(perm) 0.949 0.2176 0.0961

No significant differences

PREVALENCE for positive non-specific gill score Fishers Exact Test: C-group vs. H-group Exposure day 1 dphe

p 0.343 0.029

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AGD gill score Average AGD score 3 dphe onwards PERMANOVA table of results Source Treatment Time Tank (Treatment) Treatment x Time Tank (Treatment) x Time Residuals Total

df 3 5 4 15 20 192 239

SS MS 218.02 72.672 97.233 19.447 0.36667 0.091667 68.733 4.5822 6.4333 0.32167 36.8 0.19167 427.58

Pseudo-F 792.79 60.456 0.47826 14.245 1.6783

P(perm) 0.0001 0.7633 0.0001 0.0398

P(MC) 0.0001

PAIR-WISE TESTS Term 'Treatment x Time' Within level '3 dphe' of factor 'time' Groups Control, hydroids Control, P.per. Control, Hydroids + P.per. Hydroids, P.per. Hydroids, Hydroids + P.per. P.per., Hydro + P.per.

t P(MC) Denominator is 0 6 0.0001 3 0.0076 6 0.0001 3 0.0079 1.4056 0.1722

Within level '7 dphe' of factor 'time' Groups Control, hydroids Control, P.per. Control, Hydroids + P.per. Hydroids, P.per. Hydroids, Hydroids + P.per. P.per., Hydro + P.per.

t P(MC) Denominator is 0 1.964 0.0668 2.3333 0.0303 1.964 0.0672 2.3333 0.0338 1.1882 0.2503

Within level '14 dphe' of factor 'time' Groups Control, hydroids Control, P.per. Control, Hydroids + P.per. Hydroids, P.per. Hydroids, Hydroids + P.per. P.per., Hydroids + P.per.

t P(MC) Denominator is 0 9 0.0001 Denominator is 0 9 0.0001 Denominator is 0 1.5 0.1539

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Within level '21 dphe' of factor 'time' Groups t Control, hydroids 1 Control, P.per. 15 Control, Hydroids + P.per. 16.5 Hydroids, P.per. 12.348 Hydroids, Hydroids + P.per. 12.6 P.per., Hydroids + P.per. 1.4056 Within level '28 dphe' of factor 'time'

P(MC) 0.3212 0.0001 0.0001 0.0001 0.0001 0.1764

Groups Control, hydroids Control, P.per. Control, Hydroids + P.per. Hydroids, P.per. Hydroids, Hydroids + P.per. P.per., Hydroids + P.per.

P(MC) 0.3308 0.0001 0.0001 0.0001 0.0001 0.1386

t 1 15.922 11 13.056 9.3915 1.5492

Within level '35 dphe' of factor 'time' Groups Control, hydroids Control, P.per. Control, Hydroids + P.per. Hydroids, P.per. Hydroids, Hydroids + P.per. P.per., Hydroids + P.per.

t 5.0138 17.335 18.974 10.04 11.196 1

P(MC) 0.0001 0.0001 0.0001 0.0001 0.0001 0.3332

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Thrombi score Exposure day + 1 dphe PERMANOVA table of results Source Treatment Time Treatment x Time Residuals Total

df 1 1 1 28 31

SS MS 7.0313 7.0313 9.0313 9.0313 7.0313 7.0313 6.875 0.24554 29.969

Pseudo-F P(perm) 28.636 0.0001 36.782 0.0001 28.636 0.0001

PAIR-WISE TESTS Term 'Treatment x Time' for pairs of levels of factor 'Treatment' Within level 'Exposure day' of factor 'Time' Groups Control. hydroids

t P(perm) Denominator is 0

Within level '1 dphe' of factor 'Time' Groups Control. hydroids

t 5.3513

P(MC) 0.0001


df SS MS 3 12.713 4.2375 5 21.387 4.2775 4 0.88333 0.22083 15 22.363 1.4908 20 5.4167 0.27083 192 42.8 0.22292 239 105.56

Pseudo-F P(perm) 19.189 15.794 0.0002 0.99065 0.4057 5.5046 0.0003 1.215 0.2534

P(MC) 0,0092

df SS MS 3 12.713 4.2375 5 21.387 4.2775 4 0.88333 0.22083 15 22.363 1.4908 212 48.217 0.22744 239 105.56

Pseudo-F P(perm) 19.189 18.807 0.0001 0.97096 0.424 6.5549 0.0001

P(MC) 0,0072

Pooled terms Tank (Treatment) x Time PERMANOVA table of results Source Treatment Time Tank (Treatment) Treatment x Time Pooled Total

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df 3 5 15 216 239

SS MS 12.713 4.2375 21.387 4.2775 22.363 1.4908 49.1 0.22731 105.56

Pseudo-F P(perm) 18.642 0.0001 18.818 0.0001 6.5585 0.0001

PAIR-WISE TESTS Term 'Treatment x Time' for pairs of levels of factor 'Treatment' Within level '3 dphe' of factor 'Time' Groups Control, Hydroids Control, P.per Control, Hydroids + P.per Hydroids, P.per Hydroids, Hydroids + P.per P.Per, Hydroids + P.per

t 6.862 1.5 5.5816 5.5317 1.0366 4.3333

P(MC) 0.0001 0.1493 0.0001 0.0001 0.3094 0.0004

t 2.2778 Negative 3.8571 2.2778 0.55709 3.8571

P(MC) 0.0365

Within level '7 dphe' of factor 'Time' Groups Control, Hydroids Control, P.per Control, Hydroids + P.per Hydroids, P.per Hydroids, Hydroids + P.per P.Per, Hydroids + P.per

0.0011 0.0334 0.5883 0.0011


t P(MC) Denominator is 0 1 0.3358 1.4056 0.1802 1 0.328 1.4056 0.1766 0.84853 0.4053


t

P(MC)

1 1.2362 1 1.2362 1.8091

0.3272 0.2297 0.3375 0.2338 0.089

Negative

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t 0.84853 Negative 1.44E-08 0.84853 0.84853 Negative

P(MC) 0.3997 1 0.3991 0.4084


Negative Negative Negative

t 1

P(MC) 0.3215

1 1

0.3387 0.3295

PREVALENCE for positive Thrombi score Fishers Exact Test: C-group vs. H-group Exposure day 1 dphe

p 0.342 0.01

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Hyperplasia score AVERAGE Hyperplasia score Exposure day + 1 dphe PERMANOVA table of results Source Treatment Time Treatment x Time Residuals Total

df 1 1 1 28 31

SS 1.5313 0.03125 1.5313 13.875 16.969

MS Pseudo-F 1.5313 3.0901 0.03125 0.063063 1.5313 3.0901 0.49554

P(perm) 0.0946 0.8315 0.0906

df 3 5 4 15 20 192 239

SS MS Pseudo-F 14.733 4.9111 147.33 24.583 4.9167 8.1492 0.13333 0.033333 0.048193 29.617 1.9744 3.2726 12.067 0.60333 0.87229 132.8 0.69167 213.93

P(perm)

df 3 5 4 15 212 239

SS MS 14.733 4.9111 24.583 4.9167 0.13333 0.033333 29.617 1.9744 144.87 0.68333 213.93

Pseudo-F 147.33 7.1951 0.04878 2.8894

P(perm)

Pseudo-F 7.3159 7.3241 2.9412

P(perm) 0.0002 0.0001 0.0004

No significant differences


0.0006 0.9961 0.0089 0.6216

P(MC) 0,0002

Pooled terms Tank (Treatment) x Time PERMANOVA table of results Source Treatment Time Tank (Treatment) Treatment x Time Residuals Total

0.0001 0.995 0.0006

P(MC) 0,0002


df 3 5 15 216 239

SS 14.733 24.583 29.617 145 213.93

MS 4.9111 4.9167 1.9744 0.6713

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PAIR-WISE TESTS Term 'Treatment x Time' for pairs of levels of factor Within level '3 dphe' of factor 'Time' Groups Control, Hydroids Control, P.per Control, Hydroids + P.per Hydroids, P.per Hydroids, Hydroids + P.per P.Per, Hydroids + P.per

t 0.67082 3.82E-08 1.3416 0.47434 0.6396 0.94868

P(MC) 0.523 1 0.1978 0.6312 0.5316 0.3548


t 0.25631 1.47E-08 0.70065 0.3046 1.1442 0.80498

P(MC) 0.8027 1 0.489 0.7621 0.2634 0.4275


t 0.46291 0.43759 1.5213 1.78E-08 2.4 2.1909

P(MC) 0.6541 0.6688 0.1473 1 0.0262 0.0365


t 0.91499 1.6348 0.3873 4.0931 1.5213 1.3007

P(MC) 0.3726 0.1214 0.7035 0.0009 0.1438 0.2061


t 1.89E-08 2.4495 2.3333 2.2283 2.0896 0.39736

P(MC) 1 0.0247 0.0319 0.0411 0.0507 0.6942

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t 0.84665 6.3258 6.5485 4.4272 4.6663 0.44721

P(MC) 0.4079 0.0001 0.0001 0.0006 0.0002 0.6585

PREVALENCE for positive Hyperplasia score Fishers Exact Test: C-group vs. H-group Exposure day 1 dphe

p 0.342 0.01

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AGD lesion score AVERAGE AGD lesion score 3 dphe onwards PERMANOVA table of results Source Treatment Time Tank (Treatment) Treatment x Time Tank (Treatment) x Time Residuals Total

df 3 5 4 15 20 192 239

SS MS Pseudo-F P(perm) 27.546 9.1819 48.97 39.237 7.8475 101.26 0.0001 0.75 0.1875 1.9565 0.101 40.179 2.6786 34.563 0.0001 1.55 0.0775 0.8087 0.709 18.4 0.095833 127.66

P(MC) 0.0013

df 3 5 4 15 212 239

SS MS Pseudo-F P(perm) 27.546 9.1819 48.97 39.237 7.8475 83.392 0.0001 0.75 0.1875 1.9925 0.0979 40.179 2.6786 28.464 0.0001 19.95 0.094104 127.66

P(MC) 0.002

Pooled terms Tank (Treatment) x Time PERMANOVA table of results Source Treatment Time Tank (Treatment) Treatment x Time Residuals Total

PAIR-WISE TESTS Term 'Treatment x Time' for pairs of levels of factor 'Treatment' Too little data available for 3, 7 and 14 dphe. Treatment groups "Control" and "Hydroids" had only 0 values Within level '21 dphe' of factor 'Time' Groups Control, Hydroids Control, P.per Control, Hydroids + P.per Hydroids, P.per Hydroids, Hydroids + P.per P.Per, Hydroids + P.per

t Denominator is 0 5 1 5 1 1,3416

P(perm)

P(MC)

0,3368 1 0,3386 1 0,6626

0,0394 0,427 0,0379 0,4192 0,3141

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t Denominator is 0 Denominator is 0 4,3333 Denominator is 0 4,3333 1

P(perm)

P(MC)

0,3234

0,0553

0,3358 1

0,0502 0,4308

P(perm)

P(MC)

0,3277

0,0092

0,3245 1

0,0076 0,4276


t Denominator is 0 Denominator is 0 11 Denominator is 0 11 1

PREVALENCE for positive AGD lesion score Fishers Exact Test*: PP- vs. H+PP group 21 dphe 28 dphe

p 0.626 0.1

*Conducted for days with sufficient data

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