Analysis of population genetic structure with RAPD markers

Abstract

Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD (random amplified polymorphic DNA) method is one such technique that has attracted widespread interest. The analysis of population structure with RAPD data is hampered by the lack of complete genotypic information resulting from dominance, since this enhances the sampling variance associated with single loci as well as induces bias in parameter estimation. We present estimators for several population-genetic parameters (gene and genotype frequencies, within- and between-population heterozygosities, degree of inbreeding and population subdivision, and degree of individual relatedness) along with expressions for their sampling variances. Although completely unbiased estimators do not appear to be possible with RAPDs, several steps are suggested that will insure that the bias in parameter estimates is negligible. To achieve the same degree of statistical power, on the order of 2 to 10 times more individuals need to be sampled per locus when dominant markers are relied upon, as compared to codominant (RFLP, isozyme) markers. Moreover, to avoid bias in parameter estimation, the marker alleles for most of these loci should be in relatively low frequency. Due to the need for pruning loci with low-frequency null alleles, more loci also need to be sampled with RAPDs than with more conventional markers, and some problems of bias cannot be completely eliminated.

Efficacy of RAPD, ISSR and DAMD markers in assessment of genetic variability and population structure of wild Musa acuminata colla

“…To estimate population genetic structure, genetic diversity parameters including the percentage of polymorphic loci (Lynch and Milligan 1994), observed number of alleles, effective number of alleles (Kimura and Crow 1964), Nei's gene diversity (Nei 1973) and Shannon index (Lewontin 1972) were calculated using the software PopGene version 1.31 (Yeh et al 1999). Estimate of gene flow (Nm) was calculated as Nm=0.5×(1−Gst)/Gst (McDermott and McDonald 1993), where Gst is the gene differentiation.…”

Rapid genetic divergence in response to 15 years of simulated climate change

“…Allele frequency estimates for globally polymorphic loci (0.05 ≤  q  ≤ 0.95) were used to calculate gene diversity (an unbiased estimate of the expected heterozygosity) for climatic and soil‐depth subpopulations at BCCIL for each study species (Lynch & Milligan, 1994; Text S2).…”

Distinction between cultivated and wild chicory gene pools using AFLP markers

“…The table was then converted into a matrix where fragments were scored as either present (1) or absent (0). Using the software AFLP-SURV v1.0 (Vekemans et al 2002, available at http://www.ulb.ac.be/sciences/ lagev), estimates of pairwise relatedness coefficients (r) were calculated between individuals according to Lynch and Milligan (1994). A principal co-ordinate (PCO) analysis was performed based on this matrix using NTSys (Rohlf 2000) and the first two axes were plotted graphically.…”

“…This procedure has been shown to produce almost unbiased estimates of allelic frequencies in dominant markers (Krauss 2000). These allelic frequencies were used as input for the analysis of genetic diversity within and between samples following the method described in Lynch and Milligan (1994 …”