2 research outputs found
Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants
The internal transcribed spacers (ITS) of the nuclear ribosomal 18Sâ5.8Sâ26S cistron continue to be the most popular non-plastid
region for species-level phylogenetic studies of plant groups despite the early warnings about their potential Xaws, which may ultimately
result in incorrect assumptions of orthology. It has been gradually realized that the alternative target regions in the nuclear genome (lowcopy
nuclear genes, LCNG) are burdened with similar problems. The consequence is that, to date, developing useful LCNG for nonmodel
organisms requires an investment in time and eVort that hinders its use as a real practical alternative for many labs. It is here
argued that ITS sequences, despite drawbacks, can still produce insightful results in species-level phylogenetic studies or when non-anonymous
nuclear markers are required, provided that a thoughtful use of them is made. To facilitate this, two series of guidelines are proposed.
One helps to circumvent problems of ITS ampliWcation from the target organism, including spurious results from contaminants,
paralogs and pseudogenes, as well as detection of sequencing artifacts. The other series helps to Wnd out causes for unresolved clades in
phylogenetic reconstruction, to integrate gene phylogenies, to distinguish horizontal transfer from lineage sorting, and to reveal if ITS
phylogeny is not a good estimate of organism phylogeny.This work has been supported by grants BOS2001-1839 (to GNF) and CGL2004-00223/BOS (to JAR) from the Spanish Ministry of Science and Education.Peer reviewe