Team 3 Plan

User Choice Power, Performance, Null, Inference

User Choice simulator questions

• marker type: any->coalescent; any but SNP->forward
• population size: large->coalescent; small->forward
• time: deep->coalescent; shallow->forward
• complex history: yes->coalescent; no->forward
• management: no->coalescent; yes->forward
• marker #: large or small->coalescent; small->forward
• ploidy: haploid or diploid->coalescent; diploid->forward
• computer capacity: any->coalescent; large->forward
• time to complete: short->; long->forward

User Choice/ setting Common parameters

• #pops
• vector of population sizes
• vector of migration rates
• marker types

• markers

• mutation rate distance across loci

• samples per population

User Choice/ setting Specific parameters: Coalescent

• vector population growth rates
• historical events (invasions, range expansions, single or multiple source)
• genetics (unlinked or linked in semi-user-specified manner)

User Choice/ setting Specific parameters: Forward

• extinction/ extirpation rates
• demographies, r or k selected
• initial allele frequencies per locus (derived from real data, derived from simulation, assume equal frequencies) *# generations
• maximum population size
• selfing rate