0.994 --SpeciationDecayConstant; //Rate at which speciation rate decays with time (does not decay if 1.0, grows if > 1)
1 --ExtinctionDecayConstant; //Rate at which extinction rate decays with time (ditto)
1.0 --EvolutionDecayConstant; //Rate at which rates of sequence evolution decay with time
2.0 --PollinationSpeciationMultiplier; //Arithmetic multiplier to speciation rate for animal pollination (lowers speciation rate if < 1.0)
1.0 --PollinationExtinctionMultiplier; //As you would expect, but extinction
1.0 --PollinationSpeciationDecayConstant; //Arithmetic multiplier to SpeciationDecayConstant for animal-pollinated things
1.0 --PollinationExtinctionDecayConstant; //Extinction
1.0 --PollinationEvolutionMultiplier; //Multiplies rate of molecular evolution for animal-pollinated things
1.0 --PollinationRangeMultiplier; //Increases (if > 1.0) geographic range tendency for animal-pollinated (reduces if < 1.0)
1.0 --DispersalSpeciationMultiplier; //These are the same things, but for dispersal
1.0 --DispersalExtinctionMultiplier;
1.0 --DispersalSpeciationDecayConstant;
1.0 --DispersalExtinctionDecayConstant
1.0 --DispersalEvolutionMultiplier
1.0 --DispersalRangeMultiplier
1.0 --StochasticRangeMultiplier //Inter-timestep random volatility in species ranges; a value of 1.0 means no variation.
0.0 --RangeImportance //Exponent on the effect of geographic range on extinction. 0.0 = no effect.
0.00 --ExtinctionPulseFreuency //Frequency of elevated extinction timesteps. 0.0 = no effect.
4.0 --ExtinctionPulseIntensity //Intensity of extinction pulses. 1.0 = extinctions have no effect.
1.0 --ExtinctionPulsePollinationSelectivity //Selectivity of extinction pulses. 1.0 = no effect; >1 means animal pollination suffers more severe extinction; <1 means animal polination means less severe extinction.
1.0 --ExtinctionPulseDispersalSelectivity //Selectivity of extinction pulses. 1.0 = no effect; >1 means animal dispersal suffers more severe extinction; <1 means animal dispersal means less severe extinction.
1.0 --TransitionRate; //Intrinsic rate of transitions (C to T, T to C, A to G, G to A), as per a Kimura two-parameter evolutionary model
1.0 --TransversionRate; //Intrinsic rate of transversions (A to C, C to G, G to T, T to A, C to A, G to C, T to G, A to T), as per a Kimura two-parameter evolutionary model
1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 --Rates of character state transitions during speciation; first and second indicies represent the state changing from, the third and fourth the state changing to; first and third are pollination, second and fourth are dispersal; 0 in all cases is wind-, and 1 is animal-. This configuration generates no character evolution.
1.0 0.01 0.01 0.01 0.01 1.0 0.01 0.01 0.01 0.01 1.0 0.01 0.01 0.01 0.01 1.0 --Rates of character state transitions during background evolution. Mechanics are the same as those for speciation.
1.0 1.0 --CladePollinationImportance[2]; //Multiplication constant on the rates of state changes TO wind (0) or animal (1) pollination.
1.0 1.0 --CladeDispersalImportance[2]; //Exactly the same as above, but for dispersal; clade tendency has no effect if this constant is 1.0, but has a stronger positive effect if > 1.0. Clades will actually move AWAY from their 'preferred' type if < 1.0.
0 --MaxSpecies; //If the simulation reaches this number of species, terminate. Ignored if 0.
0 --MaxClades; //If the simulation reaches this number of clades, terminate. Ignored if 0.
64 --MaxTimesteps; //When the simulation has run for this number of timesteps, terminate. Ignored if 0 (not recommended, as it may run on forever).
1.0 --MaxSpeciesExtinction; //When this proportion of the total number of species that have become extinct reaches this value, terminate.
1.0 --MaxCladeExtinction; //As above, but for clades.


Only the numbers at the beginning of each line before the hyphens are actually necessary; everything else is comments. Hyphens do not create comments, however; including hyphenated comments will cause the program to abort and print this file (the position of the numbers in each line is what matters). Similarly, the program does not read after the MaxCladeExtinction variable, so additional comments can be put here without aborting the program.

Be advised, however: rates of speciation, extinction, and evolution input into this model are not the actual rates (the true rates are modified by range, pollination, dispersal, and time, as determined by other parameters above).