Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring.

ABSTRACT:

Background

Since the transfer and application of modern sequencing technologies to the analysis of amplified fragment-length polymorphisms (AFLP), evolutionary biologists have included an increasing number of samples and markers in their studies. Although justified in this context, the use of automated scoring procedures may result in technical biases that weaken the power and reliability of further analyses.

Results

Using a new scoring algorithm, RawGeno, we show that scoring errors--in particular "bin oversplitting" (i.e. when variant sizes of the same AFLP marker are not considered as homologous) and "technical homoplasy" (i.e. when two AFLP markers that differ slightly in size are mistakenly considered as being homologous)--induce a loss of discriminatory power, decrease

SUBMITTER: Arrigo N 

PROVIDER: S-EPMC2656475 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature