Empirical assessment of RAD sequencing forinterspecific phylogeny
2014
Cruaud, Astrid | Gautier, Mathieu, | Galan, Maxime | Foucaud, Julien | Sauné, Laure | Genson, Guénaëlle | Dubois, Emeric | Nidelet, Sabine | Deuve, Thierry | Rasplus, Jean Yves
Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current bioinformatic and phylogenetic tools produced 400x more sites than our Sanger approach (2,262,825 nt/species), fully resolving relationships between 18 species of ground beetles (divergences up to 17 My). This suggests that RAD-seq is promising to infer phylogeny of eukaryotic species, though potential biases need to be evaluated and new methodologies developed to take full advantage of such data.
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