Add/edit a coral model

Set a name for the coral model:

Set Connectivity Model

Connectivity model preset:

Set Adaptive Model (optional)

Define an adaptive model?

Adaptive model preset:
Environmental Variable:

Study area control panel

This panel allows you to choose on which region to work on. For the moment, only the reefs of New Caledonia are available.

The panel also allows to choose the background map type.

Digital reef control panel

The digital reef represents a group of corals of different type ("coral models") for which the connectivity and adaptive potential indices are computed.

This panel resumes the coral models added to the digital reef.
If you want to add a new coral model, click on the button.
For every coral model, the table shows:

the name of the coral model
the environmental variable used in the adaptive model (env)
the maximal-Fst recommended thresholds (inbound: Fst-I, outbound: Fst-O)
a button to edit the coral model ()
a button to remove the coral model ()
a checkbox () to decide whether to use or not the coral model in the indices computation

Coral model editing panel

A coral model represents a particular type of coral species or population. It is described by two parameters: the connectivity model and the adaptive model.

Connectivity Model

The connectivity model describes how the coral model is expected to disperse. It is defined by the relationship between sea-distance (a standardized metric based on sea current movements elaborated during the SABLE project) and Fst (a standard measure of genetic differentiation between populations). Every coral species has a different relationship between Fst and sea-distance, depending on the dispersal capabilities. This relationship can be evaluated through seascape genetics experiments. The connectivity model preset allows you to access connectivity models based on this kind of studies. You can use the buttons under the graph (,,) to create a custom connectivty model or modify an existing one.

Adaptive Model

Adaptive model is optional and required only for the computation of the Adaptive Potential Index (API). This kind of model describes the probability of carrying an adaptive trait/genotype given a determined range of a specific environmental variable. This kind of models are discovered in seascape genomics experiments. You can use the "Adaptive model preset" dropdown menu to select an existing adaptive model found during the SABLE project. You can use the buttons under the graph (,,) to create a custom adaptive model or modify an existing one.

Indices selection control panel

In this panel you can choose which index to compute. Five different options are available:

Inbound Connectivity Index (ICI): describes how each reef is expected to receive dispersal from other reefs.
Outbound Connectivity Index (OCI): describes how each reef is expected to disperse towards other reefs.
Adaptive Potential Index (API): describes how each reef is expected to be adapted to a specific climatic constraints.
Inbound Connectivity Index of Marine Protected Areas (MPA-ICI): an interactive mode. After drawing marine protected areas (MPA) on the map, this mode computes the ICI from these areas.
Inbound Connectivity Index of Coral Nurseries (CN-ICI): an interactive mode. The user can add to the map the emplacement of coral nurseries at specific reef. This mode then computes the ICI from these sites.

Inbound Connectivity Index (ICI) computation

The Inbound Connectivity Index (ICI) describes the estimated dispersal towards each reef of the study area. This index is based on the connectivity models of coral models in the digital reef.

For a specific reef, the ICI represents the total area of the surrounding reefs that can disperse towards the specific reef. The maximal distance of "surrounding reefs" depends on the Fst threshold (Fst-I) specified before computation.

A low Fst threshold will account for the reefs closely surrounding a focal reef, while a higher value will include further reefs in the calculation. The Fst threshold should not exceed the recommended value, in order to avoid bias due to border effects.

A high ICI indicates a reef receiving dispersal from a large reef surface, while a low ICI a reef receiving limited dispersal (i.e. potentially isolated reef).

If you want to compare ICI for different coral models, or different digital reefs, make sure to use a common Fst threshold (not exceeding the recommended values) and to set fixed limits in the color scale by clicking on the corresponding checkbox ().

Outbond Connectivity Index (OCI) computation

The Outbound Connectivity Index (OCI) describes the estimated dispersal from each reef of the study area. This index is based on the connectivity models of coral models in the digital reef.

For a specific reef, the OCI represents the total area of the surrounding reefs that can disperse to from the specific reef. The maximal distance of "surrounding reefs" depends on the Fst threshold specified (Fst-O) before computation.

A low Fst threshold will account for the reefs closely surrounding a focal reef, while a higher value will include further reefs in the calculation. The Fst threshold should not exceed the recommended value, in order to avoid bias due to border effects.

A high OCI indicates a reef dispersing to a large reef surface (i.e. potential source for the reef system), while a low OCI a reef with limited dispersal potential.

If you want to compare OCI for different coral models, or different digital reefs, make sure to use a common Fst threshold (not exceeding the recommended values) and to set fixed limits in the color scale by clicking on the corresponding checkbox ().

Adaptive Potential Index (API) computation

The Adaptive Potential Index (API) describes the estimated adaptive potential for every reef of the study area. This index is based on the adaptive model of corals in the digital reef.

For a specific reef, the API represents the probability of adaptation to a specific climatic constraint.

If more than one coral is present in the digital reef panel, the API represents the average probability between all the corals in the digital reef. In this case, be aware that the adaptive models describing the digital reef should be based on the same environmental variables.

If you want to compare API for different coral models, or different digital reefs, make sure to leave fixed limits in the color scale.

Inbound Connectivity Index of Marine Protected Areas (MPA-ICI) computation

The MPA-ICI allows to estimate the potential dispersal from marine protected areas (MPAs) set-ups defined by the user.

By clicking on the button, the user can draw one or polygon representing MPAs. The algorithm then computes Inbound Connectivity Index (ICI) from these areas. The button allows to remove MPAs previously drawn. The ICI describes the estimated dispersal towards each reef of the study area. This index is based on the connectivity models of coral models in the digital reef.

For a specific reef, the MPA-ICI represents the total area of the surrounding reefs inside the MPAs that can disperse towards the specific reef. The maximal distance of "surrounding reefs" depends on the Fst threshold (Fst-I) specified before computation.

A low Fst threshold will account for the reefs closely surrounding a focal reef, while a higher value will include further reefs in the calculation. The Fst threshold should not exceed the recommended value, in order to avoid bias due to border effects.

A high MPA-ICI indicates a reef receiving dispersal from a large reef surface of the MPAs, while a low MPA-ICI a reef receiving limited dispersal from the MPAs.

If you want to compare MPA-ICI for different coral models, different digital reefs or different MPA set-ups, make sure to use a common Fst threshold (not exceeding the recommended values) and to set fixed limits in the color scale by clicking on the corresponding checkbox ().

Inbound Connectivity Index of Coral Nurseries (CN-ICI) computation

The CN-ICI allows to estimate the potential dispersal from coral nurseries (CNs) emplacements defined by the user.

By clicking on the button, the user can select on which reef(s) to establish a CN. The algorithm then computes Inbound Connectivity Index (ICI) from this reef(s). The button allows to remove CNs previously added. The ICI describes the estimated dispersal towards each reef of the study area. This index is based on the connectivity models of coral models in the digital reef.

For a specific reef, the CN-ICI represents the total area of the surrounding reefs set as CNs that can disperse towards the specific reef. The maximal distance of "surrounding reefs" depends on the Fst threshold (Fst-I) specified before computation.

A low Fst threshold will account for the reefs closely surrounding a focal reef, while a higher value will include further reefs in the calculation. The Fst threshold should not exceed the recommended value, in order to avoid bias due to border effects.

A high CN-ICI indicates a reef receiving dispersal from a large reef surface of reefs set as CN, while a low CN-ICI a reef receiving limited dispersal from the CNs.

If you want to compare CN-ICI for different coral models, different digital reefs or different CNs emplacements, make sure to use a common Fst threshold (not exceeding the recommended values) and to set fixed limits in the color scale by clicking on the corresponding checkbox ().

DRAPEAU

Select study area

Digital Reef Panel