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Improving AFLP analysis of large-scale patterns of genetic variation – a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow

Journal Article

Ley AC; Hardy OJ

2013

Molecular Ecology

doi: 10.1111/mec.12214

AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes an improvement over classical scoring error rates which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore using a quantitative genetics framework we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion although we showed that AFLP markers might be substantially affected by nongenetic factors their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.

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Support

The Liana Ecology Project is supported by Marquette University and funded in part by the National Science Foundation.