Computing genetic similarity coefficients from RAPD data: the effects of PCR artifacts.

Abstract

Random amplified polymorphic DNA (RAPD) markers have been used for many types of genetic analyses, including genome mapping, genotype fingerprinting, phylogeny reconstruction, and measuring genetic similarities. They suffer from one potential limitation, however, because the PCR that is used to produce informative amplification products often produces artifactual products as well. Optimization of PCR protocols to eliminate artifactual bands completely is often too costly or too timeconsuming to be practical. Other methods for handling RAPD artifacts, such as deleting inconsistent or faint bands or using only those bands that are reproducible, introduce false negatives into the data. Simply ignoring artifacts and using all bands introduces false positives. When RAPD data are used to compute genetic similarity coefficients, such artifacts can cause significant bias in the estimation. The three coefficients most widely used with RAPD data, the simple matching coefficient, Jaccard's coefficient and Nei and Li's coefficient, differ in the amount of bias produced by a given level of artifactual bands. The simple matching coefficient and Nei and Li's coefficient always exhibit less percent bias than Jaccard's coefficient. For closely related organisms, Nei and Li's coefficient displays less percent bias than the simple matching coefficient. If new DNA samples possessing RAPD markers not present in the previously analyzed samples are added to a study, values of the simple matching coefficient will need to be computed for all samples, not just the new ones. Jaccard's and Nei and Li's coefficients, however, will not need to be recomputed. Furthermore, only Nei and Li's coefficient has a direct biological meaning (it is an estimate of the expected proportion of amplified fragments shared by two samples hecause they were inherited from a common ancestor). On the basis of these results, Nei and Li's coefficient is recommended for routine computation of genetic similarities using RAPD data, particularly if PCR artifacts are present.Random amplified polymorphic DNA (RAPD) markers ~ are well-established genetic tools. They have been used for genomic mapping and linkage analysis, ~3-6~ phylogeny reconstruction, ~7' 8~ genotype fingerprinting and identification, ~9-~4~ and determining genetic relationships, similarities, and genetic variation. (ls--17) RAPD bands are produced by PCR, using a single random primer that amplifies segments of DNA flanked by two primer-binding regions that theoretically are exactly complementary to the primer. The primer-binding sites must be close enough that amplification proceeds over the entire DNA segment spanning them. Because of base pair mismatch, though, a single base change in the genomic DNA can prevent amplification. ~2~ Most often, polymorphisms between different DNA samples occur when a segment that is amplified in a sample whose primer-binding site is exactly complementary to the primer is not amplified in another sample whose priming site is not an exact complement to the primer/2'18...

Sibling species or poecilogony in the polychaete Scoloplos armiger?

“…The advantage of Nei-Li distance estimates is that Total no. of individuals 91 they use only the shared presence of a band (assuming homology) (Nei and Li 1979;Harris 1999), which is appropriate for RAPD data (Lamboy 1994;Wolfe and Liston 1998). That is, since RAPD bands are scored as dominant markers, the presence of a band implies that the priming sites on either side of the fragment are present.…”

Detection of RAPD Markers Correlated with Chloroquine Resistance in Plasmodium falciparum

“…The RAPD technique generates complex banding patterns and it is therefore necessary to use a similarity coefficient to analyze this data. We used the NL coefficient (Nei and Li 1979), which is recommended for routine computation of genetic similarities (Lamboy 1994).…”

“…This analysis provided interesting data about the genomic distance between different strains. The NL coefficient was used because it is recommended for routine computation of genetic similarities using RAPD data (Lamboy 1994).…”

“…The RAPD technique generates complex banding patterns and it is therefore necessary to use a similarity coefficient to analyze this data. We used the NL coefficient (Nei and Li 1979), which is recommended for routine computation of genetic similarities (Lamboy 1994).The analysis using the NL coefficient shows a correlation between the IC 50 values of the P. falciparum strains and the profiles obtained with the three selected primers. Taken together, these results permit the classification of the strains into three groups.…”

“…This analysis provided interesting data about the genomic distance between different strains. The NL coefficient was used because it is recommended for routine computation of genetic similarities using RAPD data (Lamboy 1994).The statistical analysis was performed using the ⌾ 2 test. It was carried out to establish whether the NL values obtained with the three selected primers allowed the seven strongly resistant strains (IC 50 > 300 nM) to associate and to differentiate this group from strains with lower IC 50 values.…”