Abstract:
:Amplified fragment length polymorphism (AFLP) fingerprint data are now commonly collected using DNA sequencers. AFLP genotypes are still often scored by eye from such data - a time-consuming, error-prone and subjective process. We present a semi-automated method of genotyping sequencer-collected AFLPs at predefined fragment locations (loci) within the fingerprint. Our method uses thresholds of AFLP-polymerase chain reaction-product fluorescence intensity (peak height) in order to: (i) exclude AFLP loci that are likely to contribute high rates of error to data sets, and (ii) determine the AFLP phenotype (fragment presence or absence) at the retained loci. Error rate analysis is an integral part of this process and is used to determine optimal thresholds that minimize genotyping error, while maximizing the numbers of retained loci. We show that application of this method to a large AFLP data set allows genotype calls that are rapid, objective and repeatable, facilitating the extraction of reliable genotype data for molecular ecological studies.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Whitlock R,Hipperson H,Mannarelli M,Butlin RK,Burke Tdoi
10.1111/j.1755-0998.2007.02073.xsubject
Has Abstractpub_date
2008-07-01 00:00:00pages
725-35issue
4eissn
1755-098Xissn
1755-0998journal_volume
8pub_type
杂志文章abstract::Estimation of demographic history from nucleotide sequences represents an important component of many studies in molecular ecology. For example, knowledge of a population's history can allow us to test hypotheses about the impact of climatic and anthropogenic factors. In the past, demographic analysis was typically li...
journal_title:Molecular ecology resources
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