Statistical power for detecting genetic divergence—organelle versus nuclear markers

Abstract

Statistical power is critical in conservation for detecting genetic differences in space or time from allele frequency data. Organelle and nuclear genetic markers have fundamentally different transmission dynamics; the potential effect of these differences on power to detect divergence have been speculated on but not investigated. We examine, analytically and with computer simulations, the relative performance of organelle and nuclear markers under basic, ideal situations. We conclude that claims of a generally higher resolving power of either marker type are not correct. The ratio R = F ST,organelle /F ST,nuclear varies between 1 and 4 during differentiation and this greatly affects the power relationship. When nuclear F ST is associated with organelle differentiation four times higher, the power of the organelle marker is similar to two nuclear loci with the same allele frequency distribution. With large sample sizes (n C 50) and several populations or many alleles per locus (C5), the power difference may typically be disregarded when nuclear F ST [ 0.05. To correctly interpret observed patterns of genetic differentiation in practical situations, the expected F ST s and the statistical properties (i.e., power analysis) of the genetic markers used should be evaluated, taking the observed allele frequency distributions into consideration.

Global Phylogeography with Mixed-Marker Analysis Reveals Male-Mediated Dispersal in the Endangered Scalloped Hammerhead Shark (Sphyrna lewini)

“…Although divergent F ST values gleaned from mitochondria are generally expected to be higher and easier to detect than nuclear F ST because of mtDNA's haploid nature and uniparental inheritance [32], the analyses used in this study show marker divergences to be attributable to sex-biased dispersal rather than differences in N e . First, the large numbers of highly polymorphic markers used in this study lend considerable power to discerning genetic structure at nuclear loci, power that is equal to or greater than mtDNA.…”

Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

“…Several pairwise comparisons using mtDNA were statistically significant (Supplementary Appendix 2), indicating that mtDNA can be a powerful marker, even at low levels of nuclear divergence (Hoarau et al, 2004;Larsson et al, 2009). …”

“…For example, it has been shown that organelle markers such as mtDNA may be more powerful for detecting differentiation in recently diverged populations and especially when migration among populations is relatively high (Larsson et al, 2009).…”

Small‐scale patterns of genetic variation in a headwater specialist mayfly: No influence of selective forest harvesting on diversity

“…Low levels of differentiation are also unlikely to be due to use of a single locus (mtDNA), as studies have demonstrated that when mtDNA variation is high (as in the present case), this locus may approximate or outperform multiple locus markers in terms of power to detect population structure (Larsson et al 2009;Schmidt et al 2011). Low levels of differentiation are not attributable to a lack of power in the analysis as power simulations demonstrated that very low F STs could be detected with our sampling design.…”