Supplementary material

Table S1. Information used as conservation features and their level of protection (CS: Conservation Status, Low: LC (Low Concern), Unfavorable; Medium: NT (Neat Threatened), Bad; High: VU (Vulnerable); EN (Endangered), Threatened. CS obtained from EUNIS, 2018, ICNF, 2013 and IUCN, 2018.

EUNIS

CodeSpecies/Habitats

Period

CSEUNIS

CSICNF

CSIUCN Level Source Obs.

1110 Sandbanks N/A unfavourable-bad Bad Mediu

m ICNF,2013

1130 Estuaries N/A unfavourable-bad Bad Mediu

mICNF,2013

1140 Mud N/A unfavourable-bad Unfavourable Low ICNF,2013

1150 Coastal lagoons* N/A unfavourable-inadequate Very bad High ICNF,2013

1160 Large shallow inlets and bays

N/A unfavourable-bad Bad Mediu

mICNF,2013

1170 ReefsN/A unfavourable-

badModerate-bad

Medium

ICNF,2013

8330 Submerged caves N/A Unknown Unknown Medium

ICNF,2013 4)

2618 Balaenotoptera acutorostrata

1951-2010 LC VU High

Halpin, 2009

ICNF,2013

1)

2621 Balaenotoptera physalus

1925-2013 NT EN High

Halpin, 2009

1)

1350 Delphinus delphis1967-2013 DD LC Mediu

m

Halpin, 2009

INAG, 2011

1)

5686 Lepidorhombus boscii

2009-2011 LC - - Low

Halpin, 2009

2)

5715 Merluccius merluccius

2009-2011 LC - Low

Halpin, 2009

2)

1351 Phocoena phocoena

1974-2010 VU VU - High INAG, 2011

1)

1349 Tursiops truncatus

1905-2012 DD LC Mediu

m

INAG, 2011Halpin, 2009

1)

2034 Stenella coeruleoalba

1968-2014 DD LC Mediu

mHalpin, 2009

1)

2029Globicephala

melas 1992-2010 DD DD LC Mediu

m

Halpin, 2009

ICNF,2013

1)

2030Grampus griseus

1975-2013 DD DD LC Mediu

m

Halpin, 2009

ICNF,2013

1)

2035Ziphius cavirostris

N/A DD DD LC Medium

Halpin, 2009

ICNF,2013

1)

3022Isurus oxyrinchus

N/A DD - VU HighAquamaps,

2017a2) 5)

5707Lophius

piscatorius N/A LC - LowAquamaps,

2017b2)5)

- Sardina 2012 NT - Mediu INAG, 2011 2)

1

EUNIS

CodeSpecies/Habitats

Period

CSEUNIS

CSICNF

CSIUCN Level Source Obs.

pilchardus m 3)

-

Sea-pen an burrowing megafauna

communities

2012 Threatened (OSPAR)High OSPAR,2017

- Lophelia pertusa reefs

2006 Threatened (OSPAR)High

OSPAR,2017

- Net Primary Production (NPP)

Spring data 2010-2014

Medium

EUCMS, 2017

6)

*priority habitat in accordance with Natura 2000 guidelines (EEA, 2007)

1) All Cetacean species are part of the Berna and Bona Convention and listed in ACCOBAMS agreement and CITES (ANEXX 2A). Due to this fact, were all considered at least as medium level or higher.

2) Species added due to reference on the report from Marine Strategy Framework Directive (MAMAOT, 2012). There were 5 species considered with low environmental state, namely: Sardina pilchardus, Lophius piscatorius, Merluccius merluccius, Lepidorhombus boscii, Isurus oxyrinchus.

3) Management plan of Sardina pilchardus (2012-2015) (DGRM,2018)4) Despite unknown status its identified in as a biodiversity refuge and important for genetic resource supply

(ICNF, 2013).5) We used data from a predicted reviewed distribution map with modelled native range map. This

information provides probabilities of occurrences. From this information, we extracted the locations with probability of occurrence higher than 85% and used it as distribution map of the species (Aquamaps, 2017).

6) Information on NPP was obtained from EU Copernicus Marine Service, 2016. Data from literature allowed to select levels of primary production on spring and summer months as the most intense for the ecosystem production on Portuguese waters (FCG, 2014; ICES, 2008). From this assumption, Net Primary Production was obtained from 2010 to 2014 Spring months. From this data we calculated the average value for each location and selected the top 30% values to be used in the model.

2

Figure S1. Habitats distribution used in the model

3

Figure S2. Species distribution used in the model

4

Figure S3. Net Primary Production average from spring data 2010-2014

References

Aquamaps, 2017a. Reviewed distribution maps for Isurus oxyrinchus native range map. Aquamaps, 2017. www.aquamaps.org, version of Aug. 2016 (last accessed 15 march 2018).

Aquamaps, 2017b. Reviewed distribution maps for Lophius piscatorius, native range map. www.aquamaps.org, version of Aug. 2016. Web. Last accessed 16 march 2018.

DGRM,2018. Sardine Fishery Management Plan. Available at: https://www.dgrm.mm.gov.pt/plano-de-gestao-da-sardinha (last accessed 19 april 2018)

EEA, 2007. Guidelines for the establishment of the Natura 2000 network in the marine environment . Application of the Habitats and Birds Directives. 112. Available at: http://ec.europa.eu/environment/nature/natura2000/marine/index_en.htm.

EUCMS, 2016. CMEMS-IBI-PUM-005-003.Atlantic IBerian Biscay Irish Ocean Biogeochemistry non assimilative hindcast (2002-2014) Ibi_ Reanalysis_Bio_005_003. EU Copernicus Marine Service.

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EUNIS, 2018. EUNIS: The European Nature Information System Available at: https://eunis.eea.europa.eu/ (last accessed 19 april 2018)

FCG, 2014. The Economic Value of Oceans and in Portugal Policy Brief the Gulbenkian Oceans.

Halpin, P.N., A.J. Read, E. Fujioka, B.D. Best, B. Donnelly, L.J. Hazen, C. Kot, K. Urian, E. LaBrecque, A. Dimatteo, J. Cleary, C. Good, L.B. Crowder, and K.D. Hyrenbach. 2009. OBIS-SEAMAP: The world data center for marine mammal, sea bird and sea turtle distributions. Oceanography 22(2):104-115.

ICES, 2008. ICES advice 2008. Report of the ICES Advisory Committee, Bay of Biscay and Western Iberian Seas.

ICNF, 2013. Rede Natura 2000 – 3º Relatório Nacional de Aplicação da Diretiva Habitats. (2007-2012) Avaliação Global do Estado de Conservação das Espécies [in portuguese].

IUCN, 2018. The IUCN Red List of Threatened Species. http://www.iucnredlist.org/ (last accessed 18/03/2018)

MAMAOT, 2012. Estratégia Marinha para a subdivisão do Continente. Ministério da Agricultura, Mar, Ambiente e Ordenamento do Território; 2012. p. 906 [in Portuguese].

INAG, 2011. POEM—Plano de Ordenamento do Espaço Marítimo, Volume 5 Tomo1: Estudos de Caracterização [in portuguese].

OSPAR, 2017. OSPAR's Data & Information Management System. Mapping habitats on the OSPAR List of Threatened and/or Declining Species and Habitats. https://www.ospar.org/work-areas/bdc/species-habitats/mapping-habitats-on-the-ospar-list-of-threatened-or-declining-species-and-habitats (last accessed 18/03/2018).

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