A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects.
BACKGROUND
A full understanding of the patterns and processes of biological diversification requires the dating of evolutionary events, yet the fossil record is inadequate for most lineages under study. Alternatively, a molecular clock approach, in which DNA or amino acid substitution rates are calibrated with fossils or geological/climatic events, can provide indirect estimates of clade ages and diversification rates. The utility of this approach depends on the rate constancy of molecular evolution at a genetic locus across time and across lineages. Although the nuclear ribosomal internal transcribed spacer region (nrITS) is increasingly being used to infer clade ages in plants, little is known about the sources or magnitude of variation in its substitution rate. Here, we systematically review the literature to assess substitution rate variation in nrITS among angiosperms, and we evaluate possible correlates of the variation.


RESULTS
We summarize 28 independently calibrated nrITS substitution rates ranging from 0.38 x 10(-9) to 8.34 x 10(-9) substitutions/site/yr. We find that herbaceous lineages have substitution rates almost twice as high as woody plants, on average. We do not find any among-lineage phylogenetic constraint to the rates, or any effect of the type of calibration used. Within life history categories, both the magnitude of the rates and the variance among rates tend to decrease with calibration age.


CONCLUSIONS
Angiosperm nrITS substitution rates vary by approximately an order of magnitude, and some of this variation can be attributed to life history categories. We make cautious recommendations for the use of nrITS as an approximate plant molecular clock, including an outline of more appropriate phylogenetic methodology and caveats against over interpretation of results. We also suggest that for lineages with independent calibrations, much of the variation in nrITS substitution rates may come from uncertainty in calibration date estimates, highlighting the importance of accurate and/or multiple calibration dates.
Kay
Kathleen M
KM
Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA. kkay@lifesci.ucsb.edu
Whittall
Justen B
JB
Hodges
Scott A
SA
D019943:Amino Acid Substitution / Q000235:genetics*; D019659:Asteraceae / Q000145:classification / Q000502:physiology; D005075:Biological Evolution; D002138:Calibration / Q000592:standards; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D016013:Likelihood Functions; D008091:Literature; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010944:Plants / Q000145:classification*; D012044:Regression Analysis; D016415:Sequence Alignment; D013997:Time Factors; D032423:Winteraceae / Q000145:classification / Q000502:physiology
D021903:DNA, Ribosomal Spacer