Table 1 Prevalence across all Atlantic salmon and eDNA collections from active farms and fallow or decommissioned (inactive) farms in the Broughton Archipelago, BC. Blanks in the S. salar column indicate that these assays were not run on S. salar tissues. To show the potential impact of lysis buffer on prevalence, values are provided for each of the two different types (Purelink vs. Rebead)–both from eDNA samples collected at active farms. Tenacibaculum finnmarkense was not assayed in S. salar tissues.

Sandlance

Ammodytes hexapterus

Marine fish

5

6.5

4.2

4.3

Herring

Clupea spp.

Marine fish

74.8

93.5

65.6

48

Anchovy

Engraulis spp.

Marine fish

59

60.6

58.2

1.1

Lamprey

Entosphenus tridentatus

Marine fish

0.1

0

0.2

0

Pollock

Gadus chalcogrammus

Marine fish

18.6

39.8

8.2

17.2

Pacifcicod

Gadus macrocephalus

Marine fish

1.1

2.6

0.4

0.4

Stickleback

Gasterosteus aculeatus

Marine fish

5.4

10

3.2

1.1

surf Smelt

Hypomesus pretiosus

Marine fish

0

0

0

0

Eulachon

Thaleichthys pacificus

Marine fish

7.4

15.6

3.4

5.7

ae_sal

Aeromonas salmonicida

Infectious agent

2.8

1.3

3

0.4

0.4

ascv

Atlantic Salmon Calicivirus

Infectious agent

52.9

14.5

36.8

3.6

1.4

ca_cl

Caligus clemensi

Infectious agent

2.7

26.4

63.2

8.4

3.2

c_b_cys

Candidatus Branchiomonas cysticola

Infectious agent

1.9

29.8

81

4.9

24.4

sch

Candidatus Syngnamydia salmonis

Infectious agent

7.7

99.9

100

99.8

99.3

ctv-2

Cutthroat Trout Virus

Infectious agent

80

19.6

46.8

6.3

0.7

env

Erythrocytic Necrosis Virus

Infectious agent

0

41

61.5

31

27.6

fa_mar

Facilispora margolisi

Infectious agent

6.4

29.4

59.7

14.6

20.8

fl_psy

Flavobacterium psychrophilum

Infectious agent

6.8

24.4

33.8

19.8

31.9

icd_spp

Ichthyobodo spp.

Infectious agent

44.9

60.6

96.1

43.2

52

icp_spp

Ichthyophonus spp.

Infectious agent

0.7

81.7

95.2

75.1

83.2

ic_mul

Ichthyophthirius multifiliis

Infectious agent

2.5

82.7

97

75.7

83.5

ku_thy

Kudoa thyrsites

Infectious agent

8.3

2.7

6.5

0.8

2.9

le_sa

Lepeophtheirus salmonis

Infectious agent

0.2

3.3

8.7

0.6

0

lo_spp

Loma spp.

Infectious agent

0.2

18.4

47.6

4.2

19

mo_vis

Moritella viscosa

Infectious agent

0.3

16.9

36.8

7.2

2.2

ne_per

Neoparamoeba perurans

Infectious agent

0

0.9

2.6

0

2.2

pa_ther

Paranucleospora theridion

Infectious agent

86

86.7

95.2

82.5

67

pa_kab

Parvicapsula kabatai

Infectious agent

0.8

4.5

10.4

1.7

2.5

pa_pse

Parvicapsula pseudobranchicola

Infectious agent

8.7

1.4

4.3

0

1.8

prv-1

Piscine Orthoreovirus

Infectious agent

78.4

17.9

36.4

8.9

1.1

pisck_sal

Piscirickettsia salmonis

Infectious agent

0.8

51.9

88.7

34

49.8

p-narnav

Putative narnavirus

Infectious agent

1.2

15.6

42.9

2.3

15.1

re_sal

Renibacterium salmoninarum

Infectious agent

0.5

1

2.2

0.4

0.4

spav-1

Salmon Pescarenavirus 1

Infectious agent

0

0

0

0

0

spav-2

Salmon Pescarenavirus 2

Infectious agent

0.2

0

0

0

0

te_dic

Tenacibaculum dicentrarchi

Infectious agent

12.9

5.5

11.3

2.7

1.1

te_fin

Tenacibaculum finnmarkense

Infectious agent

56.7

87

42

10

te_mar

Tenacibaculum maritimum

Infectious agent

20.4

27.1

36.4

22.6

0.4

vi_ang

Vibrio anguillarum

Infectious agent

0

0

0

0

0

vi_sal

Aliivibrio salmonicida

Infectious agent

0

0.3

0.9

0

0

vhsv

Viral Hemorrhagic Septicemia Virus

Infectious agent

0.1

5.5

16.5

0.2

1.1

ye_ruc

Yersinia ruckeri

Infectious agent

0.1

1.4

3

0.6

0.7

Ongo_ATP6

Oncorhynchus gorbuscha

Salmonid

2.7

2.6

2.7

2.9

Onke_ATP6

Oncorhynchus keta

Salmonid

4.7

12.6

0.8

5.4

Onki_CYTB

Oncorhynchus kisutch

Salmonid

11.5

19

7.8

9.3

Onmy_COI

Oncorhynchus mykiss

Salmonid

2.3

2.6

2.1

1.8

Onne_COIII

Oncorhynchus nerka

Salmonid

5.8

4.3

6.5

4.3

Onts_COI

Oncorhynchus tshawytscha

Salmonid

25.8

58.9

9.7

10

Sasa_COI

Salmo salar

Salmonid

95.3

98.7

93.7

43.4