Empirical assessment of RAD sequencing for interspecific phylogeny.
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.
INRA, UMR1062 CBGP, Montferrier-sur-Lez, France.
Astrid
A
Cruaud
Mathieu
M
Gautier
Maxime
M
Galan
Julien
J
Foucaud
Laure
L
Sauné
Gwenaëlle
G
Genson
Emeric
E
Dubois
Sabine
S
Nidelet
Thierry
T
Deuve
Jean-Yves
JY
Rasplus
D000818:Animals; D001517:Coleoptera / Q000145:classification / Q000235:genetics; D004247:DNA / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
D004272:DNA, Mitochondrial; D004247:DNA
Carabidae; Insecta; empirical data; next-generation sequencing; phylogenomics; restriction-site associated DNA sequencing