TYPE OF MODELS
if this fIgure looks odd to you, go to How models are built in PHRAPL and read about how parameters are assigned to models in PHRAPL. You can also see the Graphic summary of model design in`PHRAPL.
Isolation Only (IO)
Models that do not include migration events, but can include multiple coalescent events, population sizes and, changes in population size. All populations/species need to coalesce at some point.
Isolation with Migration (IM)
These are the most flexible models that can be explored in PHRAPL. These models can include coalescent events, multiple migration rates, different population sizes, and changes in population size (e.g. exponential growth). It is not required for all populations/species to coalesce. But if a population does not coalesce with others, it needs to be connected by migration. Migration rates between populations can be symmetric or asymmetric and can change over time. For example, migration may be constant or occur either recently (secondary contact) or at early stages of divergence (speciation with gene flow). See AddEventToMigrationArray for more info on how to build these type of models.
Constant migration
Migration between populations or from one population to another constantly occurs at the same rate.
Ancestral migration
Migration only occurs after divergence, but it stops at some point and does not occur in the present. Specify when migration stopped using the arguments addedEventTimeand addedEventTimeAsScalarin the GridSearchfunction.
Secondary contact
Migration stopped after divergence, but it started at some point and still occurs in the present. Specify when migration started using the arguments addedEventTimeand addedEventTimeAsScalarin the GridSearchfunction.
Migration Only (MO)
Models that do not include coalescent events but can consist of multiple migration rates, population sizes, and changes in population size.
Species limits
Models that test the existance a given number of species. To analyze these models, rather than adding parameters or editing a migrationArray, hypotheses are specified using the argument setCollapseZero in the GridSearchfunction. Models with fully resolved trees are required (e.g. isolation only models).