Data from: A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research

Despite much discussion of the importance of quantifying and reporting
genotyping error in molecular studies, it is still not standard practice
in the literature. This is particularly a concern for amplified fragment
length polymorphism (AFLP) studies, where differences in laboratory,
peak-calling and locus-selection protocols can generate data sets varying
widely in genotyping error rate, the number of loci used and potentially
estimates of genetic diversity or differentiation. In our experience,
papers rarely provide adequate information on AFLP reproducibility, making
meaningful comparisons among studies difficult. To quantify the extent of
this problem, we reviewed the current molecular ecology literature (470
recent AFLP articles) to determine the proportion of studies that report
an error rate and follow established guidelines for assessing error.
Fifty-four per cent of recent articles do not report any assessment of
data set reproducibility. Of those studies that do claim to have assessed
reproducibility, the majority (~90%) either do not report a specific error
rate or do not provide sufficient details to allow the reader to judge
whether error was assessed correctly. Even of the papers that do report an
error rate and provide details, many (≥23%) do not follow recommended
standards for quantifying error. These issues also exist for other marker
types such as microsatellites, and next-generation sequencing techniques,
particularly those which use restriction enzymes for fragment generation.
Therefore, we urge all researchers conducting genotyping studies to
estimate and more transparently report genotyping error using existing
guidelines and encourage journals to enforce stricter standards for the
publication of genotyping studies.