ArticleGenetics2008
Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- Agromorphologic, genetic and methylation profiling of Dioscorea and Musa species multiplied under three micropropagation systems.PloS one · 2019Article
- Methylation divergence of invasiveEcology and evolution · 2018Article
- AFLP reveals low genetic diversity of the bryozoanJournal of biological research (Thessalonike, Greece) · 2017Article
- Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon.PloS one · 2017Article
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- Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Frontiers in plant science · 2017Article
- Differential Resistance Mechanisms to Glyphosate Result in Fitness Cost forFrontiers in plant science · 2017Article
- Genome methylation patterns across castes and generations in a parasitoid wasp.Ecology and evolution · 2016Article
- Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication.Molecular ecology · 2016Review
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- Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico.PloS one · 2016Article
- AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect.Frontiers in plant science · 2016Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP homoplasy on its effectiveness. The results indicate that the biases produced by homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15-25%) may occur with approximately 50-100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP homoplasy can produce a reduction of up to 15% in the power to detect selective loci.
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