Key for the different values of stac that can be used
in DAISIE objects, and how they can be specified in the function
DAISIE_dataprep.
stac stands for “status of the clade” formed by the
immigrant. It is an important part of DAISIE objects that informs the
likelihood functions about the endemicity status and type of data
available for each insular clade. Each colonisation event that has
extant species on the island needs to have a stac value
specified.
| stac | Input for DAISIE_dataprep table “Clade_Name” | Type of species or clade | Input for DAISIE_dataprep table “Branching_times” | Colonisation times |
|---|---|---|---|---|
| 1 | Non_endemic_MaxAge | Non-endemic species | Maximum age of colonisation | Colonisation time is unknown (either max age or age of the island can be inputed) |
| 2 | Endemic | Endemic singleton or Endemic radiation | Precise colonisation time. Any branching times | Precise colonisation time is known |
| 3 | Endemic&Non_endemic | Endemic species/clade and one or more re-colonisations of the same mainland species | Precise colonisation time, Any additional colonisation times and branching times. | Precise colonisation times are known (but most recent colonisation is ignored) |
| 4 | Non_endemic | Non-endemic species | Precise colonisation time | Precise colonisation time is known |
| 5 | Endemic_MaxAge | Endemic singleton or Endemic radiation | Maximum age of colonisation | Colonisation time is unknown (either max age or age of the island can be inputed). In the case of a radiation, there are no branching times available, and the additional cladogenetic species are added as missing. |
| 6 | Endemic_MaxAge | Endemic radiation | Maximum age of colonisation. At least one branching time. | Colonisation time is unknown but at least one branching time is available. The 1st branching event (crown age) is used as the minimum colonisation time. |
| 7 | Endemic&Non_endemic_MaxAge | Endemic species/clade and one or more re-colonisations of the same mainland species | Maximum age of colonisation. Any additional colonisation times and branching times. | Oldest colonisation time is unknown (most recent colonisation is ignored) |
| 8 | Non_endemic_MaxAgeMinAge | Non-endemic species | Maximum age of colonisation. Minimum age of colonisation. | Colonisation time unknown (either max age or age of the island can be inputed). Minimum colonisation time known |
| 9 | Endemic_MaxAgeMinAge | Endemic singleton | Maximum age of colonisation. Minimum age of colonisation. | Colonisation time unknown (either max age or age of the island can be inputed). Minimum colonisation time known |