Supporting Information. Jansen, J., P. K. Dunstan, N. A. Hill, P. Koubbi, J. Melbourne-Thomas, R. Causse, and C. R. Johnson. 2020. Integrated assessment of the spatial distribution and structural dynamics of deep benthic marine communities. Ecological Applications.

Appendix S1

Figure S1 Observed total counts of demersal fish per main feeding-type and species archetype. The underlying maps indicate the spatial distribution of the probability of occurrence for each species archetype. The big aggregation of zoobenthos-feeding fish in SA-B is a school of Trematomus tokarevi.

Appendix S1: Page 1 Figure S2 Observed total abundances of benthic macro-invertebrates per main feeding-type and species archetype from Jansen et al. (2018a). The underlying maps indicate the spatial distribution of the probability of occurrence for each species archetype. OTUs= Operational taxonomic units (= species or other groups of morphologically resembling fauna identified to the highest possible taxonomic resolution). Letters F-K identify each species archetype and are identical to the letters used in Fig. 5.

Appendix S1: Page 2 Figure S3 Predicted values from the species archetype models versus observed values from the sample-sites (the probability of occurrence across all species in each species archetype). The red dotted line indicates the 1:1 line between predicted and observed values; the R2-value is for a linear regression between observed and predicted values. The predictions are based on trawl-data from 68 sites. From top to bottom: SA-A (Species Archetype - A) to SA-E

SA-A

SA-B

SA-C

SA-D

SA-E

Appendix S1: Page 3 Figure S4 Hard classed distribution of five species archetype predictions for demersal fish across the George V shelf, East Antarctica. Map (a) identifies which group of species is most likely to be encountered at any specific prediction point across the study area. (b) shows the probability of occurrence for the most likely archetype.

Appendix S1: Page 4 Figure S5 Hard classed categorisation of the George V shelf, East Antarctica from kmeans clustering of the species archetype models of both demersal fish and benthic invertebrates. K-means clustering on four clusters is done using the probability of occurrence of each species archetype (both invertebrates and fish) in each cell of the environmental raster. Note the clustering based on the species archetype models does not separate out the shallow-steep habitat well when comparing only depth and slope of the sample sites (only 2 and 4 sample-locations for invertebrates and fish respectively). Map (a) show the distribution of the four habitats. Plot (b) shows the categorisation of each sample with respect to the depth and slope of the seafloor.

Appendix S1: Page 5 Figure S6 Cross-comparison of changes in macro-invertebrate and fish functional groups between major Antarctic benthic habitats. The top-right part of the figure shows the change between habitats for each functional group, as predicted from the qualitative network model (the difference in total positive outcomes after 10000 press-perturbations). The bottom-left shows the observed change in functional group abundances from sample sites located in the different habitats (see Appendix S1: Figure S5 and methods for details on the calculation).

Appendix S1: Page 6 Table S1 Taxonomic family, species identity, feeding-type and associated species archetype (where species archetype association is ≥ 0.8; colour coded for easier interpretation) for each demersal fish-species used in this study. The last column identifies the source used to identify the feeding-type. Sub-families are identified for the Nototheniidae (Nototh.). * = feeding-type information from unpublished data

Family Species Feeding-type Species Archetype Reference Nototh. - Artedidraconidae loennbergi zoobenthos SA-E (wide distr., medium depth) www.fishbase.se Nototh. - Artedidraconidae Artedidraco shackletoni zoobenthos SA-D (banks) www.fishbase.se Nototh. - Artedidraconidae Artedidraco skottsbergi zoobenthos SA-D (banks) www.fishbase.se Nototh. - Artedidraconidae Dolloidraco longedorsalis zoobenthos SA-A (basins - common species) www.fishbase.se Nototh. - Artedidraconidae Histiodraco velifer zooplankton SA-D (banks) www.fishbase.se Nototh. - Artedidraconidae Pogonophryne phyllopogon zoobenthos SA-D (banks) Lombarte et al. (2003) Nototh. - Artedidraconidae Pogonophryne maculatus zoobenthos SA-B (basins - rare species) Lombarte et al. (2003) Nototh. - Artedidraconidae Pogonophryne sp. zoobenthos SA-B (basins - rare species) Lombarte et al. (2003) Nototh. - Bathydraconidae Acanthodraco dewitti Nototh. - Bathydraconidae Akarotaxis nudiceps SA-A (basins - common species) www.fishbase.se Nototh. - Bathydraconidae Bathydraco antarcticus SA-B (basins - rare species) Nototh. - Bathydraconidae Bathydraco macrolepis SA-B (basins - rare species) www.fishbase.se Nototh. - Bathydraconidae Bathydraco marri SA-B (basins - rare species) Nototh. - Bathydraconidae Cygnodraco mawsoni nekton SA-D (banks) www.fishbase.se Nototh. - Bathydraconidae Gerlachea australis zooplankton SA-A (basins - common species) www.fishbase.se Nototh. - Bathydraconidae Gymnodraco acuticeps nekton SA-D (banks) www.fishbase.se Nototh. - Bathydraconidae Prionodraco evansii zoobenthos SA-D (banks) www.fishbase.se Nototh. - Bathydraconidae Racovitzia glacialis zooplankton SA-E (wide distr., medium depth) www.fishbase.se Nototh. - Bathydraconidae Vomeridens infuscipinnis SA-A (basins - common species) www.fishbase.se Nototh. - Chaenodraco wilsoni zooplankton SA-B (basins - rare species) www.fishbase.se Nototh. - Channichthyidae Chionobathyscus dewitti zooplankton SA-C (shelf-break) www.fishbase.se Nototh. - Channichthyidae Chionodraco hamatus nekton SA-E (wide distr., medium depth) www.fishbase.se Nototh. - Channichthyidae Chionodraco myersi zooplankton SA-B (basins - rare species) www.fishbase.se Nototh. - Channichthyidae zooplankton SA-E (wide distr., medium depth) www.fishbase.se Nototh. - Channichthyidae Dacodraco hunteri SA-B (basins - rare species) www.fishbase.se Nototh. - Channichthyidae Neopagetopsis ionah zooplankton SA-C (shelf-break) www.fishbase.se Nototh. - Channichthyidae macropterus nekton SA-D (banks) www.fishbase.se Nototh. - Channichthyidae Pagetopsis maculatus nekton SA-D (banks) www.fishbase.se; * Nototh. - Nototheniidae Trematomus eulepidotus zooplankton SA-E (wide distr., medium depth) www.fishbase.se Nototh. - Nototheniidae Trematomus hansoni zooplankton www.fishbase.se Nototh. - Nototheniidae Trematomus lepidorhinus/loennbergii zoobenthos SA-E (wide distr., medium depth) Nototh. - Nototheniidae Trematomus newnesi zooplankton SA-B (basins - rare species) www.fishbase.se Nototh. - Nototheniidae Trematomus pennellii zoobenthos SA-D (banks) www.fishbase.se Nototh. - Nototheniidae Trematomus scotti zooplankton SA-E (wide distr., medium depth) www.fishbase.se Nototh. - Nototheniidae Trematomus tokarevi zoobenthos SA-B (basins - rare species) www.fishbase.se Liparidae Careproctus longipectoralis zoobenthos SA-C (shelf-break) Duhamel et al. (2010) Liparidae Edentoliparis terraenovae zooplankton SA-B (basins - rare species) Duhamel et al. (2010) Liparidae Paraliparis antarcticus zoobenthos SA-B (basins - rare species) Duhamel et al. (2010) Liparidae Paraliparis charcoti zoobenthos SA-B (basins - rare species) Duhamel et al. (2010) Liparidae Paraliparis leobergi zoobenthos SA-D (banks) Duhamel et al. (2010) Liparidae Paraliparis mawsoni zoobenthos SA-C (shelf-break) Duhamel et al. (2010) Liparidae Paraliparis valentinae zoobenthos Duhamel et al. (2010) Macrouridae Macrourus whitsoni zoobenthos SA-C (shelf-break) www.fishbase.se Muraenolepididae Muraenolepis sp. zooplankton SA-C (shelf-break) Zoarcidae Lycenchelys antarcticus zoobenthos Duhamel et al. (2010) Zoarcidae Lycenchelys aratrirostris zoobenthos SA-B (basins - rare species) Duhamel et al. (2010) Zoarcidae Lycenchelys tristichodon zoobenthos SA-B (basins - rare species) Duhamel et al. (2010) Zoarcidae Lycenchelys xanthoptera zoobenthos SA-C (shelf-break) Duhamel et al. (2010) Zoarcidae Lycodapus pachysoma zooplankton SA-C (shelf-break) Duhamel et al. (2010) Zoarcidae Lycodichthys antarcticus zoobenthos SA-D (banks) Duhamel et al. (2010) Zoarcidae Oidiphorus mcallisteri zoobenthos SA-C (shelf-break) Duhamel et al. (2010) Zoarcidae Ophthalmolycus amberensis zoobenthos SA-A (basins - common species) Duhamel et al. (2010) Zoarcidae Pachycara brachycephalus zoobenthos SA-B (basins - rare species) Duhamel et al. (2010) Zoarcidae Pachycara sp. zoobenthos Duhamel et al. (2010)

Appendix S1: Page 7 Table S2 Notes and some relevant references for the signed interaction nodes in the qualitative network diagram. P=positive, N=negative, uncertain or weak links marked in grey.

From To sign Notes reference High export ratios for primary production and Surface-derived food near Pelagic food sources P particulate organic carbon in the Southern Henson et al. (2012) seafloor Ocean Surface-derived food near Depth of seafloor N Decomposition of food-particles during sinking seafloor Same volume of water moving over shallow Depth of seafloor Tidal-current speed N areas induces higher tidal-current speeds Slope of seafloor Food-deposition / sedimentation N Particles less likely to settle on sloped surfaces Slope of seafloor Hard substratum P Particles less likely to settle on sloped surfaces Ocean-current speed Suspended food P Ocean-currents resuspend food-particles Jansen et al. (2018b) Ocean-current speed Food-deposition / sedimentation N Ocean-currents resuspend food-particles Jansen et al. (2018b) Tidal-current speed Suspended food P Ocean-currents resuspend food-particles Jansen et al. (2018b) Tidal-current speed Food-deposition / sedimentation N Ocean-currents resuspend food-particles Jansen et al. (2018b) Surface-derived food near seafloor Food-deposition / sedimentation P More particles -> more sedimentation Surface-derived food near seafloor Suspended food P More particles -> more resuspension Hard substrata decrease with food-deposition, Food-deposition / sedimentation Hard substratum N but uncertain how strong this link is relative to the strong link between hard substrata and slope Deposit feeders are more abundant where Food-deposition / sedimentation Mobile deposit feeders P Jansen et al. (2018b) sedimentation is higher Strength of link uncertain. Deposition of food has Food-deposition / sedimentation Sessile suspension feeders N been shown to influence suspension feeder Jansen et al. (2018b) abundance less than suspended food Suspension feeders are more abundant where Suspended food Sessile suspension feeders P Jansen et al. (2018b) suspended food is abundant Hard substratum Mobile deposit feeders N Deposit feeders prefer soft substrata Suspension feeders need hard substrata for Hard substratum Sessile suspension feeders P attachment Mobile deposit feeders Zoobenthos feeding fish P / N Predator-prey interaction Mobile deposit feeders Mobile predators P / N Predator-prey interaction Sessile suspension feeders Mobile predators P Provide habitat, but strength of link uncertain Sessile suspension feeders Zoobenthos feeding fish P Provide habitat, but strength of link uncertain Mobile predators Zoobenthos feeding fish P / N Predator-prey interaction Predator-prey interaction, but size of the negative effect of zooplankton feeding fish on Pelagic food sources Zooplankton feeding fish P zooplankton unknown, and therefore not included here Predator-prey interaction, but role of each prey Zoobenthos feeding fish Nekton feeding fish P / N source and the strength of link uncertain Predator-prey interaction, but role of each prey Zooplankton feeding fish Nekton feeding fish P / N source and the strength of link uncertain

Appendix S1: Page 8 Table S3 Setup of press-perturbations of the dynamic network model. Using QPress, both depth and slope are given either positive (+) or negative (-) press-perturbations for simulating changes in the ecosystem between the four main habitats.

Press-perturbation Change in ecosystem Main occurrence of the habitat Depth Slope characteristics + + Deeper & steeper Shelf-break and slope + - Deeper & more level Shelf-depressions and Sills - + Shallower & steeper Edges of the banks and along the coastline - - Shallower & more level Top of the banks

Table S4 Proportional abundances of different feeding types of demersal fish and benthic macro-invertebrates in each broad habitat identified using the Species Archetype Models. Values are calculated in three steps: First, k-means clustering for a target of four clusters is done using the probability of occurrence of each species archetype (both invertebrates and fish) in each cell of the environmental raster. Second, sample locations within each individual cluster are used to calculate average abundances for each feeding types in that cluster. Third, proportional abundances for each feeding type are calculated. Comic-icons above the table support quick identification of the habitat. The clustering based on the species archetype models did not separate out the shallow-steep habitat well enough to allow robust analysis (only 2 and 4 sample-locations for invertebrates and fish respectively), which is why we do not discuss this habitat further.

shallow-flat deep-flat deep-steep shallow-steep invertebrates Suspension feeder 0.704 0.653 0.644 0.672 Deposit feeder 0.047 0.084 0.062 0.047 Predator 0.14 0.135 0.164 0.203 Unknown 0.11 0.129 0.13 0.078

fish Plankton feeder 0.233 0.391 0.385 0.412 Benthos feeder 0.693 0.446 0.486 0.588 Nekton feeder 0.04 0.078 0.094 0 Unknown 0.034 0.084 0.036 0

Appendix S1: References

Duhamel, G., M. Hautecoeur, A. Dettai, R. Causse, P. Pruvost, F. Busson, A. Couloux, P. Koubbi, R. Williams, C. Ozouf-Costaz, and G. Nowara. 2010. Liparids from the Eastern sector of Southern Ocean and first information from molecular studies. Cybium 34:319-343. Henson, S. A., R. Sanders, and E. Madsen. 2012. Global patterns in efficiency of particulate organic carbon export and transfer to the deep ocean. Global Biogeochemical Cycles 26:GB1028. Jansen, J., N. A. Hill, P. K. Dunstan, M. P. Eléaume, and C. R. Johnson. 2018a. Taxonomic Resolution, Functional Traits, and the Influence of Species Groupings on Mapping Antarctic Seafloor Biodiversity. Frontiers in Ecology and Evolution 6:81. Jansen, J., N. A. Hill, P. K. Dunstan, J. McKinlay, M. D. Sumner, A. L. Post, M. P. Eleaume, L. K. Armand, J. P. Warnock, B. K. Galton-Fenzi, and C. R. Johnson. 2018b. Abundance and richness of key Antarctic seafloor fauna correlates with modelled food availability. Nature Ecology and Evolution 2:71-80. Lombarte, A., I. Olaso, and A. Bozzano. 2003. Ecomorphological trends in the Artedidraconidae (Pisces: : ) of the Weddell Sea. Antarctic Science 15:211-218.

Appendix S1: Page 9