Bryan Danforth is an assistant professor in the Department of Entomology. His current research focuses on molecular and morphological approaches to insect systematics. This paper was prepared while Danforth was a National Science Foundation Postdoctoral Fellow with G. C. Eickwort. Corey Freeman-Gallant is a doctoral candidate in Ecology and Evolutionary Biology. His research examines sexual selection and male parental care in double-brooded passerines.
DNA fingerprinting data and the problem of non-independence among pairwise comparisons
Article first published online: 22 SEP 2009
Volume 5, Issue 2, pages 221–227, April 1996
How to Cite
DANFORTH, B. N. and FREEMAN-GALLANT, C. R. (1996), DNA fingerprinting data and the problem of non-independence among pairwise comparisons. Molecular Ecology, 5: 221–227. doi: 10.1046/j.1365-294X.1996.00080.x
- Issue published online: 22 SEP 2009
- Article first published online: 22 SEP 2009
- Received 15 January 1995 revised 30 May 1995 accepted 20 October 1995
- DNA fingerprinting;
- population structure
Multilocus DNA fingerprinting is commonly used to assess genetic similarity within and between geographically disjunct populations. Typically, the proportion of DNA fingerprinting bands shared between two individuals (SXY) is calculated for all possible pair-wise comparisons and the resulting data analysed parametrically to test differences in mean band-sharing among groups. The degree to which covariation among interdependent SXY values (Sab - Sbc) biases the analyses is often unknown. Here, we assess the extent of covariation in four DNA fingerprinting studies and evaluate the effectiveness of two corrective procedures, a permutation test and a subsampling routine using only independent pairwise comparisons drawn without replacement from the overall data. Covariation among interdependent SXY values was significantly greater than zero in every data set examined, including those from a bee, a rodent, and two passerine birds. Permutation tests did not correct for interdependence and yielded significance values nearly identical to those derived from uncorrected parametric procedures. In contrast, the subsampling procedure yielded corrected estimates of the standard error that were two to four times larger than those derived parametrically. As a result, comparisons that were significant using parametric tests were either non-significant or only marginally significant with the subsampling routine. We conclude that interdependence among SXY values poses a substantial obstacle to hypothesis testing that must be addressed in future studies.