Table 6.

Major assumptions of and questions relating to inference of migration or population size, and their implications in population genetic studies using microsatellites

Method	Assumption or question	References	Related issues	References
Migration
BayesAss	Gametic linkage equilibrium within populations	Wilson and Rannala (2003)	Detects shifts in gametic linkage equilibrium to estimate recent migration	Wilson and Rannala (2003)
BayesAss	Low migration rate; immigrants comprise less than one-third of population	Faubet et al. (2007)	When assumptions are violated, inferences using microsatellites may be accurate only for low migration rates (<0.01) and high differentiation (FST > 0.1)	Faubet et al. (2007)
BayesAss	Migration and drift are constant during past few generations	Faubet et al. (2007)
GENECLASS2	Detection of first generation migrants only. Assumes sexual reproduction	Paetkau et al. (2004), Piry et al. (2004)	–	–
Population size
BOTTLENECK	Infinite allele model, stepwise mutation model, or two-phase mutation model	Piry et al. (1999)	Reports on sensitivity to mutation model conflict	Cornuet and Luikart (1996), Leblois et al. (2006), Peery et al. (2012)
BOTTLENECK	Infinite allele model, stepwise mutation model, or two-phase mutation model	Piry et al. (1999)	Low power of test may limit their utility	Peery et al. (2012)
M-ratio	Generalized stepwise mutation model	Garza and Williamson (2001)	Can significantly overestimate bottlenecks when mutation parameters are improperly specified	Peery et al. (2012)
M-ratio	Generalized stepwise mutation model	Garza and Williamson (2001)	Low power of test may limit their utility	Peery et al. (2012)
MSVAR	Stepwise mutation model	Beaumont (1999)	Reports on sensitivity to mutation model conflict	Girod et al. (2011), Faurby and Pertoldi (2012)