A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects.

BMC Evolutionary Biology
Kathleen M KayScott A Hodges

Abstract

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. 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...Continue Reading

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Citations

Feb 21, 2008·Heredity·S A Hodges, J B Whittall
Oct 21, 2009·Proceedings of the National Academy of Sciences of the United States of America·W Scott ArmbrusterBruce G Baldwin
Mar 23, 2010·Proceedings of the National Academy of Sciences of the United States of America·Stephen A SmithMichael J Donoghue
Jul 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·R Toby PenningtonColin E Hughes
Sep 25, 2009·Proceedings. Biological Sciences·Stephen A Smith, Jeremy M Beaulieu
Jan 6, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Elena M Kramer, Scott A Hodges
Oct 4, 2008·Science·Stephen A Smith, Michael J Donoghue
Dec 1, 2010·BMC Evolutionary Biology·Terezie MandákováMartin A Lysak
Sep 24, 2008·BMC Evolutionary Biology·H Thorsten LumbschAna Crespo
May 22, 2009·BMC Evolutionary Biology·Heidi M MeudtDavid Bryant
Dec 18, 2013·Systematic Biology·Stephan NylinderArne A Anderberg
Oct 3, 2014·Proceedings. Biological Sciences·S AbrahamczykS S Renner
Apr 5, 2008·Molecular Phylogenetics and Evolution·Lyn G CookMichael D Crisp
Aug 26, 2016·Scientific Reports·Guo-Feng JiangJoeri Sergej Strijk

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Software Mentioned

nrITS
MODELTEST
BRUNCH
PAUP
R8S
CAIC
Phylomatic
ClustalX
Phylogenetic Independence

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