Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization.

ABSTRACT: INFERRING PHYLOGENETIC RELATIONSHIPS BETWEEN CLOSELY RELATED TAXA CAN BE HINDERED BY THREE FACTORS: (1) the lack of informative molecular variation at short evolutionary timescale; (2) the lack of established markers in poorly studied taxa; and (3) the potential phylogenetic conflicts among different genomic regions due to incomplete lineage sorting or introgression. In this context, Restriction site Associated DNA sequencing (RAD-seq) seems promising as this technique can generate sequence data from numerous DNA fragments scattered throughout the genome, from a large number of samples, and without preliminary knowledge on the taxa under study. However, divergence beyond the within-species level will necessarily reduce the number of conserved and non-duplicated restriction sites, and there

SUBMITTER: Cariou M 

PROVIDER: S-EPMC3631399 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature