Temporal variability in sea lice population connectivity and implications for regional management protocol

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1 The following supplement accompanies the article Temporal variability in sea lice population connectivity and implications for regional management protocol Thomas P. Adams*, Dmitry Aleynik, Kenneth D. Black *Corresponding author: Aquaculture Environment Interactions 8: (2016) Fig. S1: Example output from particle tracking model. (a) Single tracks from each salmon aquaculture site within the model domain. Sites and respective tracks are coloured based upon their northing coordinate. (b) Relative proportion of time spent by particles in each model element, per unit area. (c) Visual representation of site connectivity matrix for a single simulation, showing connections above a threshold of

2 Fig. S2: Mean logarithm of connectivity between active sites, FMAs, DMAs and FHMRAs on the west coast of Scotland (sites/management units arranged south to north), omitting connections below a threshold probability of Connectivity is relative to maximum for each particular configuration. 2

3 Fig. S3: Weak clusters of all (active and inactive) sites (linked by connections either to or from one another) created by including only mean connections greater than a range of thresholds. (a) C ij > (b) C ij > (b) C ij >0.01. Sites are coloured by cluster (in (c), several geoegraphically separated clusters share the same colour). 3

4 Fig. S4: Strong active site clusters (sites linked by connections to AND from one another) created by including only mean connections greater than a range of thresholds. (a) Cij> (b) Cij>0.01. Sites are coloured by cluster; sites in the same cluster and located together are coloured similarly (different clusters share colours, as clusters are physically small in this scenario). 4

5 Management units in Scottish Salmon aquaculture Table S1: List of industry Farm Management Areas with locality description, coordinates of polygon centroid calculated in ArcGIS (UTM Zone 30N), and whether they fall within the hydrodynamic model domain. Code Locality x (m) y (m) Included S1 Haroldswick, Shetland N S2 Bluemull sound, Shetland N S3 Hascosay Sound, Shetland N S4 Yell Sound, Shetland N S5 Dury Voe, Whalsay, Sheltand N S6 Out Skerries, Shetland N S7 Ronas Voe, Shetland N S8a St Magnus Bay north, Shetland N S8b St Magnus Bay south, Shetland N S9 West Mainland N S10 Gruting Voe, Shetland N S11 The Deeps, Shetland N O1 Westray, Orkney N O4 Holm Sound, Orkney mainland N O2 Stronsay Firsth, Westray Firth, Orkney N M1 Loch Eriboll N M2 Loch Inchard Y M3 Loch Laxford Y M5 Bagh Chalbha, Eddrachillis Bay Y M6 Loch a'chairn Bhain, Eddrachillis Bay Y M4 Badcall Bay Y M7 Eddrachillis Bay Y M8 Clashnessie Bay, Oldany Y M9 Enard Bay Y M10 Summer Isles Y M11 Loch Kanaird, Isle Martin, Ardmair Y M12 Loch Broom Y M13 Annat Bay Y M14 Gruinard Bay, Little Loch Broom Y M15 Loch Ewe Y M16 Loch Gairloch Y M17 Loch Torridon, Loch Shieldaig Y M18 Loch Arnish, Raasay Y M26 Loch Portree Y M19 Loch Kishorn Y M20 Loch Carron Y M21 Loch Alsh, Loch Duich Y M28 Loch Ainort Y M24 Loch Snizort Y M25 Loch Dunvegan Y M27 Loch Bracadale Y M29 Loch Slapin, Loch Eishort Y M22 Loch Hourn Y M23 Loch Nevis Y M30 Arisaig, Morar Y M31 Loch Ailort Y M32 Loch Moidart Y M34 Loch Sunart, Kilchoan Y M35 Sound of Mull Y M36 Loch Linnhe south, Kerrera, Loch Etive, Creran Y M33 Loch Linnhe north, Loch Leven, Loch Eil Y M37 Loch Tuath, Loch na Keal Y M38 Loch Scridain Y M39 Loch Spelve Y M40 Seil Sound, Loch Melfort, Loch Craignish Y 5

6 Code Locality x (m) y (m) Included M41 Loch Sween Y M44 Loch Caolisport Y M42 Loch Fyne Y M45 Kyle of Bute Y M43 Loch Striven Y M46 Gigha Y M49 Machrihanish Bay, Kintyre Y M47 Kilbrannan Sound, Arran Y M48 Lamlash Bay Y W2 West Loch Roag, Lewis N W1 East Loch Roag, Lewis N W3 Loch Erisort, Lewis Y W4 Loch Ouirm, Lewis Y W5 Loch Shell, Lewis Y W6 Loch Seaforth, Lewis Y W8 East Loch Tarbert Y W9 Loch Stocanais, Loch Ghreosabhagh, Harris Y W10 Loch Fhionnsabhaigh, Harris Y W7 West Loch Tarbert N W12 Lochmaddy Y W11 Sound of Harris south Y W13 Loch Euphoirt, North Uist Y W14 Ronay, North Uist Y W15 Loch Uiskevagh, Benbecula Y W16 Benbecula south Y W17 Loch Carnan, South Uist Y W18 Loch Skipport, South Uist Y W19 Loch Eyenort, South Uist Y W20 Loch Boisdale, South Uist Y W21 Barra north Y W22 Castle Bay, Barra Y Table S2: List of Marine Scotland Disease Management Areas with coordinates of polygon centroid calculated in ArcGIS (UTM Zone 30N) and whether they fall within the hydrodynamic model domain. Code x (m) y (m) Included 7C Y 7B Y 7A Y 5C Y 6B N 5B Y 6A N 5A Y 9A N 9B Y 9C Y 10A Y 10B Y 10D Y 10C Y 11A Y 11B Y 12A Y 12B Y 12C Y 14A Y 14B Y 14C Y 6

7 Code x (m) y (m) Included 15C Y 15A Y 15E Y 15B Y 16A Y 16E Y 16C Y 16D Y 19A Y 18A Y 18B Y 19B Y 19C Y Y 18C Y 8C N 8A N 8B N 3A N 3B N 4A N 2A N 2C N 1D N 4B N 1B N 1A N 4C N 2B N 7

8 Table S3: List of Scottish Salmon Producers Organisation Fish Health Management Reporting Areas with name, coordinates of polygon centroid calculated in ArcGIS (UTM Zone 30N), and whether they fall within the hydrodynamic model domain. Code Name x (m) y (m) Included 42 Fyne Y 43 Ruel and Drummachloy Y 41 Carradale and Iorsa Y 38 Add and Ormsary Y 40 Islay and Jura Y 37 Awe and Nell Y 36S Sanda to Creran South Y 36N Sanda to Creran North Y 39 Island of Mull Y 33 Morar to Shiel Y 35 Sunart and Aline Y 32 Glenelg to Kilchoan Y 31 Loch Long and Croe Y 30 Kishorn and Carron Y 29 Badachro to Applecross Y 34N Skye and Small Isles North Y 34S Skye and Small Isles South Y 27 Kennart to Gruinard Y 28 Ewe Y 26S Inchard to Kirkaig South Y 26N Inchard to Kirkaig North Y 25 Hope and Grudie Y 58E Isle of Lewis East Y 59 Harris Y 58W Isle of Lewis West N 60N The Uists North Y 60S The Uists South Y 61 Orkney N 62W Shetland West N 62E Shetland East N 8