Abstract
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 400× 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.
Keywords:
Carabidae; Insecta; empirical data; next-generation sequencing; phylogenomics; restriction-site associated DNA sequencing.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Animals
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Coleoptera / classification
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Coleoptera / genetics
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DNA / genetics
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DNA, Mitochondrial / genetics
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Evolution, Molecular*
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High-Throughput Nucleotide Sequencing / methods
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Molecular Sequence Data
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Phylogeny*
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Sequence Analysis, DNA / methods*
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Species Specificity
Associated data
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