Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed Tit (Parus monticolus) to explore the resolving ability of these two types of markers. The south-western and central mitochondrial DNA (mtDNA) phylogroups were divergent to some extent in sequence-based nuclear data, while mixed together in microsatellites data. The F ST values among clades were about four times lower in microsatellite loci than those in sequence-based nuclear loci. We are of the opinion that size homoplasy may have contributed to the inability of microsatellites to uncover differentiation. Our results suggest that sequence-based nuclear loci outperformed microsatellite loci in detecting population structures, especially those focused on populations with large effective population sizes. There was no significant correlation between F ST values and allelic size variability, which suggested that the efficiency of microsatellite loci in detecting genetic structure may be independent of their polymorphism. F ST is better than R ST in detecting intraspecific divergence due to the high variance of R ST . In agreement with sequence-based nuclear loci, microsatellite loci did resolve the genetic distinctness of the Taiwan Residents phylogroup. The genetic differentiation between the Taiwan Residents and continental clades may involve allopatric divergence without gene flow.
