Protocols Script


The 11 protocols developed by the project aim to detect different types of changes in ecosystems and biodiversity, as well as environmental changes caused by temperature. Homogeneous and standardised monitoring is essential to track climate change both in our marine protected areas and throughout the Mediterranean Sea.

These protocols were tested and implemented in several locations in the Cap de Creus Natural Park and the Natura 2000 area of the Litoral del Baix Empordà throughout the autumn of 2020.




The temperature of the water column is measured every 5 meters from -5 to -40 meters. 


  • Annual temperature cycle between -5 and -40 m in the localities studied between January and October 2021: 
  • Stratification Charts: A common pattern of water column stratification is observed with a thermocline located around -15/-20 m. During the months of July and August, the thermocline shows changes in position and can reach -30 or more meters.
  • Exposure to high temperatures or number of days with temperatures above 24°C at different seabeds during July, August and September 2020: a temperature of 24°C is considered the thermotolerance limit for many benthic species, especially for in the main gorgonian species, such as the red gorgonian, Paramuricea clavata (Crisci et al., 2017). Some days were detected when the temperature exceeded 24°C at a depth of between 15 and 20 meters.  

© Quim Garrabou 




This protocol assesses the impact of mass mortality events on the main gorgonian species and other habitat-forming species. 

The number of healthy colonies/individuals and the number of affected colonies (>10% affected) are quantified, and the percentage of affected colonies and the type affectation or mortality (recent or old) are estimated.


  • Most populations have more than 10% mortality and, therefore, are considered impacted and their status is unfavourable.
  • In general, the percentage mortality of the populations studied decreases at depth, where there is less impact of the increase in temperature, although mortality is observed in all the depth ranges evaluated.
  • The most commonly recorded type of mortality was epibiosis (ancient mortality), although recent mortality was also detected. This indicates that most of the impacts on the populations are not recent, but come from other impacts, such as Storm Gloria.
© Cristina Linares

PROTOCOL 3, 4 and 6

LEK 1-2-3: Local Ecological knowledge

These are protocols based on surveys of historical knowledge and the daily activities of local fishermen. 

PROTOCOL 3 – LEK 1: LOCAL ECOLOGICAL KNOWLEDGE-1 Historical fish trends and georeferenced records

Description: This protocol aims to recover historical information on changes in the abundance and distribution of species and facilitate the early detection of new species that appear in areas where they were not previously present. 

PROTOCOL 4 – LEK 2 – Periodic monitoring of fish and georeferenced records

Description: This protocol aims to obtain qualitative information about species that can be used as reliable indicators of climate change to facilitate the early detection of new species (both native and exotic) appearing in areas where they were not previously present. 


Description: This protocol aims to recover historical information about the episodes of mass mortality of marine organisms, often linked to specific climatic conditions, mainly fish, filtering organisms and sessile invertebrates.  




This protocol studies and quantifies the abundance of fish species in the Mediterranean and defines a “tropicalisation index” based on the ratio of cold water species versus warm water species. 


This protocol has been shown to be effective in recording the densities of the most abundant species of fish in the two protected areas and ruling out the presence of other species of clear tropical affinity.

The different localities have similar species present and differences in species abundance.

A greater proportion of cold water species has been observed: Coris julius vs. Thalassoma pavo and Serranus cabrilla vs. Serranus Scriba, although a beginning of southernisation can be sensed, it is slightly more pronounced in the LBE. 




This protocol defines the state of conservation of the Posidonia oceanica meadows by assessing shoot density.


The density of Posidonia oceanica shoots obtained is high in the Cap de Creus Natural Park, where the density values (400-600 shoots/m2) lie within the reference values of previous studies, and show a good state of the phanerogamous meadows in this area. On the contrary, the density in the Natura 2000 area of the Litoral del Baix Empordà was lower (between 300-400 shoots/m2) and was lower than the reference values of previous studies, indicating that the meadows in this space are not in a good state.

No remarkable differences between populations were observed in each protected area, although, in the places where the meadows were continuous (Caials in the Cap de Creus Natural Park, and Punta de sa Claveguera in the Natura 2000 area of the Litoral del Baix Empordà), the density values recorded were higher. This fact could be due to the fact that continuous meadows favour the state of marine phanerogamous meadows.

The flowering of P. oceanica takes place, mainly, between the months of September and November. Despite having carried out the sampling at this time, flowers were only found in Cap Roig (Litoral del Baix Empordà), with a high density.

© Cristina Linares




This protocol assesses the state of health of mother-of-pearl Pinna nobilis, populations. 


No living individuals were found with the protocol, given the high mortality present throughout the Mediterranean. A pair of dead mother-of-pearls were found: one in Punta de sa Claveguera and the other in Sa Tuna.

Due to the low density of individuals of Pinna nobilis, the protocol described for carrying out the census is laborious and makes it difficult to identify individuals outside the study area. In specific citizen science monitoring actions carried out recently at the PNCCR, live mother-of-pearl specimens were found in the bay of Cadaqués (approx. 11) and also further north.

© Jordi Riera




This protocol determines the abundance and size structure of the sea urchin species Paracentrotus lividus and Arbacia lixula. When the density of sea urchins is higher than 200 individuals per 10 m2, habitats are likely to change from habitats dominated by macroalgae to underwater deserts.


Differences were observed between the two protected areas, with a higher density of individuals of A. lixula recorded in the Cap de Creus Natural Park. Conversely, higher density values of P. lividus were obtained in Litoral del Baix Empordà, especially in the town of Sa Tuna. The Cap de Creus Natural Park area is characterised by a cold thermal regime, so the presence and abundance of the thermophilic species A. lixula could be an indicator of thermal anomalies and a gradual warming of the area.

The size structure of the two species was different. Medium-sized individuals of A. lixula were found, and a more homogeneous structure, with small individuals, for P. lividus. The lack of small-sized individuals of A. lixula could be due to the greater abundance of predatory fish in the Cap de Creus Natural Park, which exert a strong pressure on their populations by eliminating the smaller sizes. 

The presence of adult-sized sea urchins hinders the re-establishment of algal forests and facilitates the formation of whitewashes and simplified algal communities. This indicator suggests that protection of the two protected areas studied is not sufficient as there is a control effect due to predation by fish.




This protocol detects invasive species through photographic analysis of different communities and specifically the coverage of different functional groups and species such as algae and sessile invertebrates. This makes it possible to determine the predominant types of habitats in each depth and locality, and the percentage coverage allows underwater deserts to be identified. 


No notable differences were observed between protected areas or between depths. However, a greater proportion of bare rock or whitewash was observed in the Natura 2000 area of the Litoral del Baix Empordà area, which may indicate a higher frequency of whitewash or habitats dominated by herbivores. Although it was initially thought that these categories would allow invasive species to be identified quickly and effectively, this was not the case.

In the locality of Sa Tuna, the presence of Caulerpa cylindracea was observed, but not during this protocol.

© Cristina Linares. UB




This protocol allows monitoring changes in the structure and complexity of habitats through Structure from Motion (SfM) photogrammetry.


This protocol is effective for studying habitat structure and complexity. However, it is in a preliminary phase and further efforts are needed to optimise and standardise the methods. In addition, we must highlight its great dependence on high-quality photographs, which is also related to having optimal visibility conditions during sampling, and therefore this protocol was difficult to carry out between the months of October and November due to the conditions of turbidity and the difficulty of subsequent analysis by project experts.

© Cristina Linares. UB