Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants

TLDR

The authors compiled 307 studies that used nuclear DNA markers to assess among‑ and within‑population genetic diversity in wild angiosperms and gymnosperms. Dominant markers (RAPD, AFLP, ISSR) produce comparable estimates, whereas STMS yields almost threefold higher within‑population diversity but similar among‑population estimates; diversity patterns are influenced by sample size, allele count, geographic distance, and life‑history traits, with long‑lived outcrossers retaining most variation within populations and annual/selfing taxa showing more among‑population variation, and overall dominant and STMS markers largely agree except for geographic‑range effects.

Abstract

Abstract A compilation was made of 307 studies using nuclear DNA markers for evaluating among‐ and within‐population diversity in wild angiosperms and gymnosperms. Estimates derived by the dominantly inherited markers (RAPD, AFLP, ISSR) are very similar and may be directly comparable. STMS analysis yields almost three times higher values for within‐population diversity whereas among‐population diversity estimates are similar to those derived by the dominantly inherited markers. Number of sampled plants per population and number of scored microsatellite DNA alleles are correlated with some of the population genetics parameters. In addition, maximum geographical distance between sampled populations has a strong positive effect on among‐population diversity. As previously verified with allozyme data, RAPD‐ and STMS‐based analyses show that long‐lived, outcrossing, late successional taxa retain most of their genetic variability within populations. By contrast, annual, selfing and/or early successional taxa allocate most of the genetic variability among populations. Estimates for among‐ and within‐population diversity, respectively, were negatively correlated. The only major discrepancy between allozymes and STMS on the one hand, and RAPD on the other hand, concerns geographical range; within‐population diversity was strongly affected when the former methods were used but not so in the RAPD‐based studies. Direct comparisons between the different methods, when applied to the same plant material, indicate large similarities between the dominant markers and somewhat lower similarity with the STMS‐based data, presumably due to insufficient number of analysed microsatellite DNA loci in many studies.